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Cheng P, Mao C, Tang J, Yang S, Cheng Y, Wang W, Gu Q, Han W, Chen H, Li S, Chen Y, Zhou J, Li W, Pan A, Zhao S, Huang X, Zhu S, Zhang J, Shu W, Wang S. Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering. Cell Res 2024; 34:630-647. [PMID: 38969803 PMCID: PMC11369238 DOI: 10.1038/s41422-024-00989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024] Open
Abstract
Mutations in amino acid sequences can provoke changes in protein function. Accurate and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but remains a fundamental challenge. To resolve this challenge, here we present Protein Mutational Effect Predictor (ProMEP), a general and multiple sequence alignment-free method that enables zero-shot prediction of mutation effects. A multimodal deep representation learning model embedded in ProMEP was developed to comprehensively learn both sequence and structure contexts from ~160 million proteins. ProMEP achieves state-of-the-art performance in mutational effect prediction and accomplishes a tremendous improvement in speed, enabling efficient and intelligent protein engineering. Specifically, ProMEP accurately forecasts mutational consequences on the gene-editing enzymes TnpB and TadA, and successfully guides the development of high-performance gene-editing tools with their engineered variants. The gene-editing efficiency of a 5-site mutant of TnpB reaches up to 74.04% (vs 24.66% for the wild type); and the base editing tool developed on the basis of a TadA 15-site mutant (in addition to the A106V/D108N double mutation that renders deoxyadenosine deaminase activity to TadA) exhibits an A-to-G conversion frequency of up to 77.27% (vs 69.80% for ABE8e, a previous TadA-based adenine base editor) with significantly reduced bystander and off-target effects compared to ABE8e. ProMEP not only showcases superior performance in predicting mutational effects on proteins but also demonstrates a great capability to guide protein engineering. Therefore, ProMEP enables efficient exploration of the gigantic protein space and facilitates practical design of proteins, thereby advancing studies in biomedicine and synthetic biology.
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Affiliation(s)
- Peng Cheng
- Bioinformatics Center of AMMS, Beijing, China
| | - Cong Mao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jin Tang
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Sen Yang
- Bioinformatics Center of AMMS, Beijing, China
| | - Yu Cheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wuke Wang
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Qiuxi Gu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Han
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Hao Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sihan Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | | | | | - Wuju Li
- Bioinformatics Center of AMMS, Beijing, China
| | - Aimin Pan
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xingxu Huang
- Zhejiang Lab, Hangzhou, Zhejiang, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Jun Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Wenjie Shu
- Bioinformatics Center of AMMS, Beijing, China.
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2
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Gao Q, Zhang C, Li M, Yu T. Protein-Protein Interaction Prediction Model Based on ProtBert-BiGRU-Attention. J Comput Biol 2024; 31:797-814. [PMID: 39069885 DOI: 10.1089/cmb.2023.0297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024] Open
Abstract
The physiological activities within cells are mainly regulated through protein-protein interactions (PPI). Therefore, studying protein interactions has become an essential part of researching protein function and mechanisms. Traditional biological experiments required for PPI prediction are expensive and time consuming. For this reason, many methods based on predicting PPI from protein sequences have been proposed in recent years. However, existing computational methods usually require the combination of evolutionary feature information of proteins to predict PPI docking situations. Because different relevant features of selected proteins are chosen, there may be differences in the predicted results for PPI. This article proposes a PPI prediction method based on the pretrained protein sequence model ProtBert, combined with the Bidirectional Gated Recurrent Unit (BiGRU) and attention mechanism. Only using protein sequence information and leveraging ProtBert's powerful ability to capture amino acid feature information, BiGRU is used for further feature extraction of the amino acid vectors output by ProtBert. The attention mechanism is then applied to enhance the focus on different amino acid features and improve the expression ability of protein sequence features, ultimately obtaining binary classification results for protein interactions. Experimental results show that our proposed ProtBert-BiGRU-Attention model has good predictive performance for PPI. Through relevant comparative experiments, it has been proven that our model performs well in protein binary prediction. Furthermore, through the ablation experiment of the model, different deep learning modules' contributions to the prediction have been demonstrated.
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Affiliation(s)
- Qian Gao
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Chi Zhang
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Ming Li
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Tianfei Yu
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China
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3
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Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenković T. Current and future directions in network biology. BIOINFORMATICS ADVANCES 2024; 4:vbae099. [PMID: 39143982 PMCID: PMC11321866 DOI: 10.1093/bioadv/vbae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/31/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024]
Abstract
Summary Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology. Availability and implementation Not applicable.
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Affiliation(s)
- Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Michelle M Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Aydin Wells
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
- Lucy Family Institute for Data and Society, University of Notre Dame, Notre Dame, IN 46556, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Deisy Morselli Gysi
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States
- Department of Statistics, Federal University of Paraná, Curitiba, Paraná 81530-015, Brazil
- Department of Physics, Northeastern University, Boston, MA 02115, United States
| | - Arjun Krishnan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, United States
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, United States
- Wisconsin Institute for Discovery, Madison, WI 53715, United States
| | - Anaïs Baudot
- Aix Marseille Université, INSERM, MMG, Marseille, France
| | - Serdar Bozdag
- Department of Computer Science and Engineering, University of North Texas, Denton, TX 76203, United States
- Department of Mathematics, University of North Texas, Denton, TX 76203, United States
| | - Danny Z Chen
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Kapil Devkota
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, United States
- Morgridge Institute for Research, Madison, WI 53715, United States
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Seattle, WA 98109, United States
| | - Pengfei Gu
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Pietro H Guzzi
- Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, Catanzaro, 88100, Italy
| | - Heng Huang
- Department of Computer Science, University of Maryland College Park, College Park, MD 20742, United States
| | - Meng Jiang
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Ziynet Nesibe Kesimoglu
- Department of Computer Science and Engineering, University of North Texas, Denton, TX 76203, United States
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, United States
| | - Mehmet Koyuturk
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, United States
| | - Nataša Pržulj
- Department of Computer Science, University College London, London, WC1E 6BT, England
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, 08010, Spain
- Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
| | - Teresa M Przytycka
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, United States
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ 08544, United States
| | - Anna Ritz
- Department of Biology, Reed College, Portland, OR 97202, United States
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, NJ 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - Donna K Slonim
- Department of Computer Science, Tufts University, Medford, MA 02155, United States
| | - Hanghang Tong
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Xinan Holly Yang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637, United States
| | - Byung-Jun Yoon
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, United States
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Haiyuan Yu
- Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, United States
| | - Tijana Milenković
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
- Lucy Family Institute for Data and Society, University of Notre Dame, Notre Dame, IN 46556, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, United States
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4
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Ko YS, Parkinson J, Liu C, Wang W. TUnA: an uncertainty-aware transformer model for sequence-based protein-protein interaction prediction. Brief Bioinform 2024; 25:bbae359. [PMID: 39051117 PMCID: PMC11269822 DOI: 10.1093/bib/bbae359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/31/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Protein-protein interactions (PPIs) are important for many biological processes, but predicting them from sequence data remains challenging. Existing deep learning models often cannot generalize to proteins not present in the training set and do not provide uncertainty estimates for their predictions. To address these limitations, we present TUnA, a Transformer-based uncertainty-aware model for PPI prediction. TUnA uses ESM-2 embeddings with Transformer encoders and incorporates a Spectral-normalized Neural Gaussian Process. TUnA achieves state-of-the-art performance and, importantly, evaluates uncertainty for unseen sequences. We demonstrate that TUnA's uncertainty estimates can effectively identify the most reliable predictions, significantly reducing false positives. This capability is crucial in bridging the gap between computational predictions and experimental validation.
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Affiliation(s)
- Young Su Ko
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States
| | - Jonathan Parkinson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States
| | - Cong Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States
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5
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Szymborski J, Emad A. INTREPPPID-an orthologue-informed quintuplet network for cross-species prediction of protein-protein interaction. Brief Bioinform 2024; 25:bbae405. [PMID: 39171984 PMCID: PMC11339867 DOI: 10.1093/bib/bbae405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated 'wet lab' experiments. In silico PPI inference methods are ideal tools to overcome these limitations, but often struggle with cross-species predictions. We present INTREPPPID, a method that incorporates orthology data using a new 'quintuplet' neural network, which is constructed with five parallel encoders with shared parameters. INTREPPPID incorporates both a PPI classification task and an orthologous locality task. The latter learns embeddings of orthologues that have small Euclidean distances between them and large distances between embeddings of all other proteins. INTREPPPID outperforms all other leading PPI inference methods tested on both the intraspecies and cross-species tasks using strict evaluation datasets. We show that INTREPPPID's orthologous locality loss increases performance because of the biological relevance of the orthologue data and not due to some other specious aspect of the architecture. Finally, we introduce PPI.bio and PPI Origami, a web server interface for INTREPPPID and a software tool for creating strict evaluation datasets, respectively. Together, these two initiatives aim to make both the use and development of PPI inference tools more accessible to the community.
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Affiliation(s)
- Joseph Szymborski
- Department of Electrical and Computer Engineering, McGill University, 845 Sherbrooke Street West, Montréal, QC H3A 0G4, Canada
- Mila, Quebec AI Institute, 6666 St-Urbain Street #200, Montréal, QC H2S 3H1, Canada
| | - Amin Emad
- Department of Electrical and Computer Engineering, McGill University, 845 Sherbrooke Street West, Montréal, QC H3A 0G4, Canada
- Mila, Quebec AI Institute, 6666 St-Urbain Street #200, Montréal, QC H2S 3H1, Canada
- The Rosalind and Morris Goodman Cancer Institute, 1160 Pine Avenue, Montréal, QC H3A 1A3, Canada
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6
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Volzhenin K, Bittner L, Carbone A. SENSE-PPI reconstructs interactomes within, across, and between species at the genome scale. iScience 2024; 27:110371. [PMID: 39055916 PMCID: PMC11269938 DOI: 10.1016/j.isci.2024.110371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/04/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Ab initio computational reconstructions of protein-protein interaction (PPI) networks will provide invaluable insights into cellular systems, enabling the discovery of novel molecular interactions and elucidating biological mechanisms within and between organisms. Leveraging the latest generation protein language models and recurrent neural networks, we present SENSE-PPI, a sequence-based deep learning model that efficiently reconstructs ab initio PPIs, distinguishing partners among tens of thousands of proteins and identifying specific interactions within functionally similar proteins. SENSE-PPI demonstrates high accuracy, limited training requirements, and versatility in cross-species predictions, even with non-model organisms and human-virus interactions. Its performance decreases for phylogenetically more distant model and non-model organisms, but signal alteration is very slow. In this regard, it demonstrates the important role of parameters in protein language models. SENSE-PPI is very fast and can test 10,000 proteins against themselves in a matter of hours, enabling the reconstruction of genome-wide proteomes.
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Affiliation(s)
- Konstantin Volzhenin
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
- Institut Universitaire de France, Paris, France
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7
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Si Y, Zou J, Gao Y, Chuai G, Liu Q, Chen L. Foundation models in molecular biology. BIOPHYSICS REPORTS 2024; 10:135-151. [PMID: 39027316 PMCID: PMC11252241 DOI: 10.52601/bpr.2024.240006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 07/20/2024] Open
Abstract
Determining correlations between molecules at various levels is an important topic in molecular biology. Large language models have demonstrated a remarkable ability to capture correlations from large amounts of data in the field of natural language processing as well as image generation, and correlations captured from data using large language models can also be applicable to solving a wide range of specific tasks, hence large language models are also referred to as foundation models. The massive amount of data that exists in the field of molecular biology provides an excellent basis for the development of foundation models, and the recent emergence of foundation models in the field of molecular biology has really pushed the entire field forward. We summarize the foundation models developed based on RNA sequence data, DNA sequence data, protein sequence data, single-cell transcriptome data, and spatial transcriptome data respectively, and further discuss the research directions for the development of foundation models in molecular biology.
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Affiliation(s)
- Yunda Si
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jiawei Zou
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yicheng Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Qi Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai 201804, China
| | - Luonan Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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8
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Sledzieski S, Kshirsagar M, Baek M, Dodhia R, Lavista Ferres J, Berger B. Democratizing protein language models with parameter-efficient fine-tuning. Proc Natl Acad Sci U S A 2024; 121:e2405840121. [PMID: 38900798 PMCID: PMC11214071 DOI: 10.1073/pnas.2405840121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/09/2024] [Indexed: 06/22/2024] Open
Abstract
Proteomics has been revolutionized by large protein language models (PLMs), which learn unsupervised representations from large corpora of sequences. These models are typically fine-tuned in a supervised setting to adapt the model to specific downstream tasks. However, the computational and memory footprint of fine-tuning (FT) large PLMs presents a barrier for many research groups with limited computational resources. Natural language processing has seen a similar explosion in the size of models, where these challenges have been addressed by methods for parameter-efficient fine-tuning (PEFT). In this work, we introduce this paradigm to proteomics through leveraging the parameter-efficient method LoRA and training new models for two important tasks: predicting protein-protein interactions (PPIs) and predicting the symmetry of homooligomer quaternary structures. We show that these approaches are competitive with traditional FT while requiring reduced memory and substantially fewer parameters. We additionally show that for the PPI prediction task, training only the classification head also remains competitive with full FT, using five orders of magnitude fewer parameters, and that each of these methods outperform state-of-the-art PPI prediction methods with substantially reduced compute. We further perform a comprehensive evaluation of the hyperparameter space, demonstrate that PEFT of PLMs is robust to variations in these hyperparameters, and elucidate where best practices for PEFT in proteomics differ from those in natural language processing. All our model adaptation and evaluation code is available open-source at https://github.com/microsoft/peft_proteomics. Thus, we provide a blueprint to democratize the power of PLM adaptation to groups with limited computational resources.
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Affiliation(s)
- Samuel Sledzieski
- AI for Good Research Lab, Microsoft Corporation, Redmond, WA98052
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | | | - Minkyung Baek
- Department of Biological Sciences, Seoul National University, Seoul08826, South Korea
| | - Rahul Dodhia
- AI for Good Research Lab, Microsoft Corporation, Redmond, WA98052
| | | | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
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9
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Yang T, Wang Y, He Y. TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences. BMC Bioinformatics 2024; 25:159. [PMID: 38643080 PMCID: PMC11032603 DOI: 10.1186/s12859-024-05780-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/12/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND MicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the identification of microRNA targets a prominent focus of research. Conventional experimental methods for identifying microRNA targets are both time-consuming and expensive, prompting the development of computational tools for target prediction. However, the existing computational tools exhibit limited performance in meeting the demands of practical applications, highlighting the need to improve the performance of microRNA target prediction models. RESULTS In this paper, we utilize the most popular natural language processing and computer vision technologies to propose a novel approach, called TEC-miTarget, for microRNA target prediction based on transformer encoder and convolutional neural networks. TEC-miTarget treats RNA sequences as a natural language and encodes them using a transformer encoder, a widely used encoder in natural language processing. It then combines the representations of a pair of microRNA and its candidate target site sequences into a contact map, which is a three-dimensional array similar to a multi-channel image. Therefore, the contact map's features are extracted using a four-layer convolutional neural network, enabling the prediction of interactions between microRNA and its candidate target sites. We applied a series of comparative experiments to demonstrate that TEC-miTarget significantly improves microRNA target prediction, compared with existing state-of-the-art models. Our approach is the first approach to perform comparisons with other approaches at both sequence and transcript levels. Furthermore, it is the first approach compared with both deep learning-based and seed-match-based methods. We first compared TEC-miTarget's performance with approaches at the sequence level, and our approach delivers substantial improvements in performance using the same datasets and evaluation metrics. Moreover, we utilized TEC-miTarget to predict microRNA targets in long mRNA sequences, which involves two steps: selecting candidate target site sequences and applying sequence-level predictions. We finally showed that TEC-miTarget outperforms other approaches at the transcript level, including the popular seed match methods widely used in previous years. CONCLUSIONS We propose a novel approach for predicting microRNA targets at both sequence and transcript levels, and demonstrate that our approach outperforms other methods based on deep learning or seed match. We also provide our approach as an easy-to-use software, TEC-miTarget, at https://github.com/tingpeng17/TEC-miTarget . Our results provide new perspectives for microRNA target prediction.
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Affiliation(s)
- Tingpeng Yang
- Peng Cheng Laboratory, Shenzhen, 518055, China
- Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Yu Wang
- Peng Cheng Laboratory, Shenzhen, 518055, China.
| | - Yonghong He
- Peng Cheng Laboratory, Shenzhen, 518055, China.
- Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China.
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10
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Si Y, Yan C. Protein language model-embedded geometric graphs power inter-protein contact prediction. eLife 2024; 12:RP92184. [PMID: 38564241 PMCID: PMC10987090 DOI: 10.7554/elife.92184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Accurate prediction of contacting residue pairs between interacting proteins is very useful for structural characterization of protein-protein interactions. Although significant improvement has been made in inter-protein contact prediction recently, there is still a large room for improving the prediction accuracy. Here we present a new deep learning method referred to as PLMGraph-Inter for inter-protein contact prediction. Specifically, we employ rotationally and translationally invariant geometric graphs obtained from structures of interacting proteins to integrate multiple protein language models, which are successively transformed by graph encoders formed by geometric vector perceptrons and residual networks formed by dimensional hybrid residual blocks to predict inter-protein contacts. Extensive evaluation on multiple test sets illustrates that PLMGraph-Inter outperforms five top inter-protein contact prediction methods, including DeepHomo, GLINTER, CDPred, DeepHomo2, and DRN-1D2D_Inter, by large margins. In addition, we also show that the prediction of PLMGraph-Inter can complement the result of AlphaFold-Multimer. Finally, we show leveraging the contacts predicted by PLMGraph-Inter as constraints for protein-protein docking can dramatically improve its performance for protein complex structure prediction.
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Affiliation(s)
- Yunda Si
- School of Physics, Huazhong University of Science and TechnologyWuhanChina
| | - Chengfei Yan
- School of Physics, Huazhong University of Science and TechnologyWuhanChina
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11
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Lin P, Li H, Huang SY. Deep learning in modeling protein complex structures: From contact prediction to end-to-end approaches. Curr Opin Struct Biol 2024; 85:102789. [PMID: 38402744 DOI: 10.1016/j.sbi.2024.102789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Protein-protein interactions play crucial roles in many biological processes. Traditionally, protein complex structures are normally built by protein-protein docking. With the rapid development of artificial intelligence and its great success in monomer protein structure prediction, deep learning has widely been applied to modeling protein-protein complex structures through inter-protein contact prediction and end-to-end approaches in the past few years. This article reviews the recent advances of deep-learning-based approaches in modeling protein-protein complex structures as well as their advantages and limitations. Challenges and possible future directions are also briefly discussed in applying deep learning for the prediction of protein complex structures.
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Affiliation(s)
- Peicong Lin
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Hao Li
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
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12
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Jia P, Zhang F, Wu C, Li M. A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond. Brief Bioinform 2024; 25:bbae162. [PMID: 38739759 PMCID: PMC11089422 DOI: 10.1093/bib/bbae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/17/2024] [Accepted: 03/31/2024] [Indexed: 05/16/2024] Open
Abstract
Proteins interact with diverse ligands to perform a large number of biological functions, such as gene expression and signal transduction. Accurate identification of these protein-ligand interactions is crucial to the understanding of molecular mechanisms and the development of new drugs. However, traditional biological experiments are time-consuming and expensive. With the development of high-throughput technologies, an increasing amount of protein data is available. In the past decades, many computational methods have been developed to predict protein-ligand interactions. Here, we review a comprehensive set of over 160 protein-ligand interaction predictors, which cover protein-protein, protein-nucleic acid, protein-peptide and protein-other ligands (nucleotide, heme, ion) interactions. We have carried out a comprehensive analysis of the above four types of predictors from several significant perspectives, including their inputs, feature profiles, models, availability, etc. The current methods primarily rely on protein sequences, especially utilizing evolutionary information. The significant improvement in predictions is attributed to deep learning methods. Additionally, sequence-based pretrained models and structure-based approaches are emerging as new trends.
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Affiliation(s)
- Pengzhen Jia
- School of Computer Science and Engineering, Central South University, 932 Lushan Road(S), Changsha 410083, China
| | - Fuhao Zhang
- School of Computer Science and Engineering, Central South University, 932 Lushan Road(S), Changsha 410083, China
- College of Information Engineering, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi 712100, China
| | - Chaojin Wu
- School of Computer Science and Engineering, Central South University, 932 Lushan Road(S), Changsha 410083, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, 932 Lushan Road(S), Changsha 410083, China
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13
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Dang TH, Vu TA. xCAPT5: protein-protein interaction prediction using deep and wide multi-kernel pooling convolutional neural networks with protein language model. BMC Bioinformatics 2024; 25:106. [PMID: 38461247 PMCID: PMC10924985 DOI: 10.1186/s12859-024-05725-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Predicting protein-protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational methods have been proposed, the utilization of sequence embeddings from protein language models, which contain diverse information, including structural, evolutionary, and functional aspects, has not been fully exploited. Additionally, there is a significant need for a comprehensive neural network capable of efficiently extracting these multifaceted representations. RESULTS Addressing this gap, we propose xCAPT5, a novel hybrid classifier that uniquely leverages the T5-XL-UniRef50 protein large language model for generating rich amino acid embeddings from protein sequences. The core of xCAPT5 is a multi-kernel deep convolutional siamese neural network, which effectively captures intricate interaction features at both micro and macro levels, integrated with the XGBoost algorithm, enhancing PPIs classification performance. By concatenating max and average pooling features in a depth-wise manner, xCAPT5 effectively learns crucial features with low computational cost. CONCLUSION This study represents one of the initial efforts to extract informative amino acid embeddings from a large protein language model using a deep and wide convolutional network. Experimental results show that xCAPT5 outperforms recent state-of-the-art methods in binary PPI prediction, excelling in cross-validation on several benchmark datasets and demonstrating robust generalization across intra-species, cross-species, inter-species, and stringent similarity contexts.
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Affiliation(s)
- Thanh Hai Dang
- Faculty of Information Technology, VNU University of Engineering and Technology, 144 Xuan Thuy, Hanoi, 10000, Vietnam.
| | - Tien Anh Vu
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Hanoi, 10000, Vietnam
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14
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Waksman T, Astin E, Fisher SR, Hunter WN, Bos JIB. Computational Prediction of Structure, Function, and Interaction of Myzus persicae (Green Peach Aphid) Salivary Effector Proteins. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:338-346. [PMID: 38171380 DOI: 10.1094/mpmi-10-23-0154-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Similar to plant pathogens, phloem-feeding insects such as aphids deliver effector proteins inside their hosts that act to promote host susceptibility and enable feeding and infestation. Despite exciting progress toward identifying and characterizing effector proteins from these insects, their functions remain largely unknown. The recent groundbreaking development in protein structure prediction algorithms, combined with the availability of proteomics and transcriptomic datasets for agriculturally important pests, provides new opportunities to explore the structural and functional diversity of effector repertoires. In this study, we sought to gain insight into the infection strategy used by the Myzus persicae (green peach aphid) by predicting and analyzing the structures of a set of 71 effector candidate proteins. We used two protein structure prediction methods, AlphaFold and OmegaFold, that produced mutually consistent results. We observed a wide continuous spectrum of structures among the effector candidates, from disordered proteins to globular enzymes. We made use of the structural information and state-of-the-art computational methods to predict M. persicae effector protein properties, including function and interaction with host plant proteins. Overall, our investigation provides novel insights into prediction of structure, function, and interaction of M. persicae effector proteins and will guide the necessary experimental characterization to address new hypotheses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Thomas Waksman
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - Edmund Astin
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - S Ronan Fisher
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - William N Hunter
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - Jorunn I B Bos
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, U.K
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15
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Ghosh S, Mitra P. MaTPIP: A deep-learning architecture with eXplainable AI for sequence-driven, feature mixed protein-protein interaction prediction. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 244:107955. [PMID: 38064959 DOI: 10.1016/j.cmpb.2023.107955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/26/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND AND OBJECTIVE Protein-protein interaction (PPI) is a vital process in all living cells, controlling essential cell functions such as cell cycle regulation, signal transduction, and metabolic processes with broad applications that include antibody therapeutics, vaccines, and drug discovery. The problem of sequence-based PPI prediction has been a long-standing issue in computational biology. METHODS We introduce MaTPIP, a cutting-edge deep-learning framework for predicting PPI. MaTPIP stands out due to its innovative design, fusing pre-trained Protein Language Model (PLM)-based features with manually curated protein sequence attributes, emphasizing the part-whole relationship by incorporating two-dimensional granular part (amino-acid) level features and one-dimensional whole-level (protein) features. What sets MaTPIP apart is its ability to integrate these features across three different input terminals seamlessly. MatPIP also includes a distinctive configuration of Convolutional Neural Network (CNN) with Transformer components for concurrent utilization of CNN and sequential characteristics in each iteration and a one-dimensional to two-dimensional converter followed by a unified embedding. The statistical significance of this classifier is validated using McNemar's test. RESULTS MaTPIP outperformed the existing methods on both the Human PPI benchmark and cross-species PPI testing datasets, demonstrating its immense generalization capability for PPI prediction. We used seven diverse datasets with varying PPI target class distributions. Notably, within the novel PPI scenario, the most challenging category for Human PPI Benchmark, MaTPIP improves the existing state-of-the-art score from 74.1% to 78.6% (measured in Area under ROC Curve), from 23.2% to 32.8% (in average precision) and from 4.9% to 9.5% (in precision at 3% recall) for 50%, 10% and 0.3% target class distributions, respectively. In cross-species PPI evaluation, hybrid MaTPIP establishes a new benchmark score (measured in Area Under precision-recall curve) of 81.1% from the previous 60.9% for Mouse, 80.9% from 56.2% for Fly, 78.1% from 55.9% for Worm, 59.9% from 41.7% for Yeast, and 66.2% from 58.8% for E.coli. Our eXplainable AI-based assessment reveals an average contribution of different feature families per prediction on these datasets. CONCLUSIONS MaTPIP mixes manually curated features with the feature extracted from the pre-trained PLM to predict sequence-based protein-protein association. Furthermore, MaTPIP demonstrates strong generalization capabilities for cross-species PPI predictions.
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Affiliation(s)
- Shubhrangshu Ghosh
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India; TCS Research, Tata Consultancy Services Limited, Kolkata, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India.
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16
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Lannelongue L, Inouye M. Pitfalls of machine learning models for protein-protein interaction networks. Bioinformatics 2024; 40:btae012. [PMID: 38200587 PMCID: PMC10868344 DOI: 10.1093/bioinformatics/btae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/24/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
MOTIVATION Protein-protein interactions (PPIs) are essential to understanding biological pathways as well as their roles in development and disease. Computational tools, based on classic machine learning, have been successful at predicting PPIs in silico, but the lack of consistent and reliable frameworks for this task has led to network models that are difficult to compare and discrepancies between algorithms that remain unexplained. RESULTS To better understand the underlying inference mechanisms that underpin these models, we designed an open-source framework for benchmarking that accounts for a range of biological and statistical pitfalls while facilitating reproducibility. We use it to shed light on the impact of network topology and how different algorithms deal with highly connected proteins. By studying functional genomics-based and sequence-based models on human PPIs, we show their complementarity as the former performs best on lone proteins while the latter specializes in interactions involving hubs. We also show that algorithm design has little impact on performance with functional genomic data. We replicate our results between both human and S. cerevisiae data and demonstrate that models using functional genomics are better suited to PPI prediction across species. With rapidly increasing amounts of sequence and functional genomics data, our study provides a principled foundation for future construction, comparison, and application of PPI networks. AVAILABILITY AND IMPLEMENTATION The code and data are available on GitHub: https://github.com/Llannelongue/B4PPI.
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Affiliation(s)
- Loïc Lannelongue
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, CB2 0BB Cambridge, United Kingdom
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CB2 0BB Cambridge, United Kingdom
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, CB2 0BB Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, CB2 0BB Cambridge, United Kingdom
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CB2 0BB Cambridge, United Kingdom
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, CB2 0BB Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, 3004 Victoria, Australia
- British Heart Foundation Centre of Research Excellence, University of Cambridge, CB2 0BB Cambridge, United Kingdom
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17
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Bernett J, Blumenthal DB, List M. Cracking the black box of deep sequence-based protein-protein interaction prediction. Brief Bioinform 2024; 25:bbae076. [PMID: 38446741 PMCID: PMC10939362 DOI: 10.1093/bib/bbae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/09/2024] [Indexed: 03/08/2024] Open
Abstract
Identifying protein-protein interactions (PPIs) is crucial for deciphering biological pathways. Numerous prediction methods have been developed as cheap alternatives to biological experiments, reporting surprisingly high accuracy estimates. We systematically investigated how much reproducible deep learning models depend on data leakage, sequence similarities and node degree information, and compared them with basic machine learning models. We found that overlaps between training and test sets resulting from random splitting lead to strongly overestimated performances. In this setting, models learn solely from sequence similarities and node degrees. When data leakage is avoided by minimizing sequence similarities between training and test set, performances become random. Moreover, baseline models directly leveraging sequence similarity and network topology show good performances at a fraction of the computational cost. Thus, we advocate that any improvements should be reported relative to baseline methods in the future. Our findings suggest that predicting PPIs remains an unsolved task for proteins showing little sequence similarity to previously studied proteins, highlighting that further experimental research into the 'dark' protein interactome and better computational methods are needed.
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Affiliation(s)
- Judith Bernett
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354, Freising, Germany
| | - David B Blumenthal
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Werner-von-Siemens-Str. 61, 91052, Erlangen, Germany
| | - Markus List
- Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 3, 85354, Freising, Germany
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18
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Lei C, Zhou K, Zheng J, Zhao M, Huang Y, He H, Yang S, Zhang Z. AraPathogen2.0: An Improved Prediction of Plant-Pathogen Protein-Protein Interactions Empowered by the Natural Language Processing Technique. J Proteome Res 2024; 23:494-499. [PMID: 38069805 DOI: 10.1021/acs.jproteome.3c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Plant-pathogen protein-protein interactions (PPIs) play crucial roles in the arm race between plants and pathogens. Therefore, the identification of these interspecies PPIs is very important for the mechanistic understanding of pathogen infection and plant immunity. Computational prediction methods can complement experimental efforts, but their predictive performance still needs to be improved. Motivated by the rapid development of natural language processing and its successful applications in the field of protein bioinformatics, here we present an improved XGBoost-based plant-pathogen PPI predictor (i.e., AraPathogen2.0), in which sequence encodings from the pretrained protein language model ESM2 and Arabidopsis PPI network-related node representations from the graph embedding technique struc2vec are used as input. Stringent benchmark experiments showed that AraPathogen2.0 could achieve a better performance than its precedent version, especially for processing the test data set with novel proteins unseen in the training data.
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Affiliation(s)
- Chenping Lei
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Kewei Zhou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jingyan Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Miao Zhao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Huang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shiping Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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19
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Sledzieski S, Kshirsagar M, Baek M, Berger B, Dodhia R, Ferres JL. Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566187. [PMID: 37986761 PMCID: PMC10659351 DOI: 10.1101/2023.11.09.566187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Proteomics has been revolutionized by large pre-trained protein language models, which learn unsupervised representations from large corpora of sequences. The parameters of these models are then fine-tuned in a supervised setting to tailor the model to a specific downstream task. However, as model size increases, the computational and memory footprint of fine-tuning becomes a barrier for many research groups. In the field of natural language processing, which has seen a similar explosion in the size of models, these challenges have been addressed by methods for parameter-efficient fine-tuning (PEFT). In this work, we newly bring parameter-efficient fine-tuning methods to proteomics. Using the parameter-efficient method LoRA, we train new models for two important proteomic tasks: predicting protein-protein interactions (PPI) and predicting the symmetry of homooligomers. We show that for homooligomer symmetry prediction, these approaches achieve performance competitive with traditional fine-tuning while requiring reduced memory and using three orders of magnitude fewer parameters. On the PPI prediction task, we surprisingly find that PEFT models actually outperform traditional fine-tuning while using two orders of magnitude fewer parameters. Here, we go even further to show that freezing the parameters of the language model and training only a classification head also outperforms fine-tuning, using five orders of magnitude fewer parameters, and that both of these models outperform state-of-the-art PPI prediction methods with substantially reduced compute. We also demonstrate that PEFT is robust to variations in training hyper-parameters, and elucidate where best practices for PEFT in proteomics differ from in natural language processing. Thus, we provide a blueprint to democratize the power of protein language model tuning to groups which have limited computational resources.
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Affiliation(s)
- Samuel Sledzieski
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge MA 02139, USA
- AI for Good Research Lab, Microsoft Corporation, Redmond WA 98052, USA
| | | | - Minkyung Baek
- Department of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge MA 02139, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge MA 02139, USA
| | - Rahul Dodhia
- AI for Good Research Lab, Microsoft Corporation, Redmond WA 98052, USA
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20
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Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear Sex Determination? Empirical Evidence from Bivalves. Mol Biol Evol 2023; 40:msad240. [PMID: 37935058 PMCID: PMC10653589 DOI: 10.1093/molbev/msad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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21
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Sledzieski S, Devkota K, Singh R, Cowen L, Berger B. TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. Bioinformatics 2023; 39:btad663. [PMID: 37897686 PMCID: PMC10640393 DOI: 10.1093/bioinformatics/btad663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/24/2023] [Accepted: 10/27/2023] [Indexed: 10/30/2023] Open
Abstract
MOTIVATION High-quality computational structural models are now precomputed and available for nearly every protein in UniProt. However, the best way to leverage these models to predict which pairs of proteins interact in a high-throughput manner is not immediately clear. The recent Foldseek method of van Kempen et al. encodes the structural information of distances and angles along the protein backbone into a linear string of the same length as the protein string, using tokens from a 21-letter discretized structural alphabet (3Di). RESULTS We show that using both the amino acid sequence and the 3Di sequence generated by Foldseek as inputs to our recent deep-learning method, Topsy-Turvy, substantially improves the performance of predicting protein-protein interactions cross-species. Thus TT3D (Topsy-Turvy 3D) presents a way to reuse all the computational effort going into producing high-quality structural models from sequence, while being sufficiently lightweight so that high-quality binary protein-protein interaction predictions across all protein pairs can be made genome-wide. AVAILABILITY AND IMPLEMENTATION TT3D is available at https://github.com/samsledje/D-SCRIPT. An archived version of the code at time of submission can be found at https://zenodo.org/records/10037674.
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Affiliation(s)
- Samuel Sledzieski
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Kapil Devkota
- Department of Computer Science, Tufts University, 177 College Avenue, Medford, MA 02155, United States
| | - Rohit Singh
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27705, United States
- Department of Cell Biology, Duke University, Durham, NC 27705, United States
| | - Lenore Cowen
- Department of Computer Science, Tufts University, 177 College Avenue, Medford, MA 02155, United States
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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22
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Xie S, Xie X, Zhao X, Liu F, Wang Y, Ping J, Ji Z. HNSPPI: a hybrid computational model combing network and sequence information for predicting protein-protein interaction. Brief Bioinform 2023; 24:bbad261. [PMID: 37480553 DOI: 10.1093/bib/bbad261] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/24/2023] Open
Abstract
Most life activities in organisms are regulated through protein complexes, which are mainly controlled via Protein-Protein Interactions (PPIs). Discovering new interactions between proteins and revealing their biological functions are of great significance for understanding the molecular mechanisms of biological processes and identifying the potential targets in drug discovery. Current experimental methods only capture stable protein interactions, which lead to limited coverage. In addition, expensive cost and time consuming are also the obvious shortcomings. In recent years, various computational methods have been successfully developed for predicting PPIs based only on protein homology, primary sequences of protein or gene ontology information. Computational efficiency and data complexity are still the main bottlenecks for the algorithm generalization. In this study, we proposed a novel computational framework, HNSPPI, to predict PPIs. As a hybrid supervised learning model, HNSPPI comprehensively characterizes the intrinsic relationship between two proteins by integrating amino acid sequence information and connection properties of PPI network. The experimental results show that HNSPPI works very well on six benchmark datasets. Moreover, the comparison analysis proved that our model significantly outperforms other five existing algorithms. Finally, we used the HNSPPI model to explore the SARS-CoV-2-Human interaction system and found several potential regulations. In summary, HNSPPI is a promising model for predicting new protein interactions from known PPI data.
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Affiliation(s)
- Shijie Xie
- College of Artificial Intelligence, Nanjing Agricultural University, No. 1 Weigang Rd, Nanjing, Jiangsu 210095, China
| | - Xiaojun Xie
- College of Artificial Intelligence, Nanjing Agricultural University, No. 1 Weigang Rd, Nanjing, Jiangsu 210095, China
| | - Xin Zhao
- Department of Hepatobiliary Surgery, Beijing Chaoyang Hospital affiliated to Capital Medical University, Beijing 100020, China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety of Ministry of Education & Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yiming Wang
- Key Laboratory of Biological Interactions and Crop Health, Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Jihui Ping
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhiwei Ji
- College of Artificial Intelligence, Nanjing Agricultural University, No. 1 Weigang Rd, Nanjing, Jiangsu 210095, China
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23
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Will I, Beckerson WC, de Bekker C. Using machine learning to predict protein-protein interactions between a zombie ant fungus and its carpenter ant host. Sci Rep 2023; 13:13821. [PMID: 37620441 PMCID: PMC10449854 DOI: 10.1038/s41598-023-40764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Parasitic fungi produce proteins that modulate virulence, alter host physiology, and trigger host responses. These proteins, classified as a type of "effector," often act via protein-protein interactions (PPIs). The fungal parasite Ophiocordyceps camponoti-floridani (zombie ant fungus) manipulates Camponotus floridanus (carpenter ant) behavior to promote transmission. The most striking aspect of this behavioral change is a summit disease phenotype where infected hosts ascend and attach to an elevated position. Plausibly, interspecific PPIs drive aspects of Ophiocordyceps infection and host manipulation. Machine learning PPI predictions offer high-throughput methods to produce mechanistic hypotheses on how this behavioral manipulation occurs. Using D-SCRIPT to predict host-parasite PPIs, we found ca. 6000 interactions involving 2083 host proteins and 129 parasite proteins, which are encoded by genes upregulated during manipulated behavior. We identified multiple overrepresentations of functional annotations among these proteins. The strongest signals in the host highlighted neuromodulatory G-protein coupled receptors and oxidation-reduction processes. We also detected Camponotus structural and gene-regulatory proteins. In the parasite, we found enrichment of Ophiocordyceps proteases and frequent involvement of novel small secreted proteins with unknown functions. From these results, we provide new hypotheses on potential parasite effectors and host targets underlying zombie ant behavioral manipulation.
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Affiliation(s)
- Ian Will
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA.
| | - William C Beckerson
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA
| | - Charissa de Bekker
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA.
- Department of Biology, Microbiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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24
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Xie L, Xie L. Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning. PLoS Comput Biol 2023; 19:e1010974. [PMID: 37590332 PMCID: PMC10464998 DOI: 10.1371/journal.pcbi.1010974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/29/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) are hetero-bifunctional molecules that induce the degradation of target proteins by recruiting an E3 ligase. PROTACs have the potential to inactivate disease-related genes that are considered undruggable by small molecules, making them a promising therapy for the treatment of incurable diseases. However, only a few hundred proteins have been experimentally tested for their amenability to PROTACs, and it remains unclear which other proteins in the entire human genome can be targeted by PROTACs. In this study, we have developed PrePROTAC, an interpretable machine learning model based on a transformer-based protein sequence descriptor and random forest classification. PrePROTAC predicts genome-wide targets that can be degraded by CRBN, one of the E3 ligases. In the benchmark studies, PrePROTAC achieved a ROC-AUC of 0.81, an average precision of 0.84, and over 40% sensitivity at a false positive rate of 0.05. When evaluated by an external test set which comprised proteins from different structural folds than those in the training set, the performance of PrePROTAC did not drop significantly, indicating its generalizability. Furthermore, we developed an embedding SHapley Additive exPlanations (eSHAP) method, which extends conventional SHAP analysis for original features to an embedding space through in silico mutagenesis. This method allowed us to identify key residues in the protein structure that play critical roles in PROTAC activity. The identified key residues were consistent with existing knowledge. Using PrePROTAC, we identified over 600 novel understudied proteins that are potentially degradable by CRBN and proposed PROTAC compounds for three novel drug targets associated with Alzheimer's disease.
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Affiliation(s)
- Li Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, New York, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, New York, United States of America
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York City, New York, United States of America
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York City, New York, United States of America
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25
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Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear sex determination? Empirical evidence from bivalves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547839. [PMID: 37461691 PMCID: PMC10349986 DOI: 10.1101/2023.07.05.547839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In bivalves, however, mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination in lineages that possess doubly uniparental inheritance (DUI). In these cases, females transmit a female mtDNA (F mtDNA) to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short non-coding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA shed a sncRNA partially within a male-specific mitochondrial gene that targeted pathways hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, non-respiratory functions and provide a first glimpse into an unorthodox sex determining system.
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Affiliation(s)
- Chase H. Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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26
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Lee M. Recent Advances in Deep Learning for Protein-Protein Interaction Analysis: A Comprehensive Review. Molecules 2023; 28:5169. [PMID: 37446831 DOI: 10.3390/molecules28135169] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Deep learning, a potent branch of artificial intelligence, is steadily leaving its transformative imprint across multiple disciplines. Within computational biology, it is expediting progress in the understanding of Protein-Protein Interactions (PPIs), key components governing a wide array of biological functionalities. Hence, an in-depth exploration of PPIs is crucial for decoding the intricate biological system dynamics and unveiling potential avenues for therapeutic interventions. As the deployment of deep learning techniques in PPI analysis proliferates at an accelerated pace, there exists an immediate demand for an exhaustive review that encapsulates and critically assesses these novel developments. Addressing this requirement, this review offers a detailed analysis of the literature from 2021 to 2023, highlighting the cutting-edge deep learning methodologies harnessed for PPI analysis. Thus, this review stands as a crucial reference for researchers in the discipline, presenting an overview of the recent studies in the field. This consolidation helps elucidate the dynamic paradigm of PPI analysis, the evolution of deep learning techniques, and their interdependent dynamics. This scrutiny is expected to serve as a vital aid for researchers, both well-established and newcomers, assisting them in maneuvering the rapidly shifting terrain of deep learning applications in PPI analysis.
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Affiliation(s)
- Minhyeok Lee
- School of Electrical and Electronics Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
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27
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Singh R, Sledzieski S, Bryson B, Cowen L, Berger B. Contrastive learning in protein language space predicts interactions between drugs and protein targets. Proc Natl Acad Sci U S A 2023; 120:e2220778120. [PMID: 37289807 PMCID: PMC10268324 DOI: 10.1073/pnas.2220778120] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/10/2023] [Indexed: 06/10/2023] Open
Abstract
Sequence-based prediction of drug-target interactions has the potential to accelerate drug discovery by complementing experimental screens. Such computational prediction needs to be generalizable and scalable while remaining sensitive to subtle variations in the inputs. However, current computational techniques fail to simultaneously meet these goals, often sacrificing performance of one to achieve the others. We develop a deep learning model, ConPLex, successfully leveraging the advances in pretrained protein language models ("PLex") and employing a protein-anchored contrastive coembedding ("Con") to outperform state-of-the-art approaches. ConPLex achieves high accuracy, broad adaptivity to unseen data, and specificity against decoy compounds. It makes predictions of binding based on the distance between learned representations, enabling predictions at the scale of massive compound libraries and the human proteome. Experimental testing of 19 kinase-drug interaction predictions validated 12 interactions, including four with subnanomolar affinity, plus a strongly binding EPHB1 inhibitor (KD = 1.3 nM). Furthermore, ConPLex embeddings are interpretable, which enables us to visualize the drug-target embedding space and use embeddings to characterize the function of human cell-surface proteins. We anticipate that ConPLex will facilitate efficient drug discovery by making highly sensitive in silico drug screening feasible at the genome scale. ConPLex is available open source at https://ConPLex.csail.mit.edu.
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Affiliation(s)
- Rohit Singh
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Samuel Sledzieski
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Bryan Bryson
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, MA02155
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
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28
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Zheng J, Yang X, Huang Y, Yang S, Wuchty S, Zhang Z. Deep learning-assisted prediction of protein-protein interactions in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:984-994. [PMID: 36919205 DOI: 10.1111/tpj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
Currently, the experimentally identified interactome of Arabidopsis (Arabidopsis thaliana) is still far from complete, suggesting that computational prediction methods can complement experimental techniques. Motivated by the prosperity and success of deep learning algorithms and natural language processing techniques, we introduce an integrative deep learning framework, DeepAraPPI, allowing us to predict protein-protein interactions (PPIs) of Arabidopsis utilizing sequence, domain and Gene Ontology (GO) information. Our current DeepAraPPI comprises: (i) a word2vec encoding-based Siamese recurrent convolutional neural network (RCNN) model; (ii) a Domain2vec encoding-based multiple-layer perceptron (MLP) model; and (iii) a GO2vec encoding-based MLP model. Finally, DeepAraPPI combines the prediction results of the three individual predictors through a logistic regression model. Compiling high-quality positive and negative training and test samples by applying strict filtering strategies, DeepAraPPI shows superior performance compared with existing state-of-the-art Arabidopsis PPI prediction methods. DeepAraPPI also provides better cross-species predictive ability in rice (Oryza sativa) than traditional machine learning methods, although the overall performance in cross-species prediction remains to be improved. DeepAraPPI is freely accessible at http://zzdlab.com/deeparappi/. In the meantime, we have also made the source code and data sets of DeepAraPPI available at https://github.com/zjy1125/DeepAraPPI.
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Affiliation(s)
- Jingyan Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaodi Yang
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Yan Huang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shiping Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, 33146, USA
- Department of Biology, University of Miami, Miami, FL, 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
- Institute of Data Science and Computing, University of Miami, Miami, FL, 33146, USA
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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29
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Durham J, Zhang J, Humphreys IR, Pei J, Cong Q. Recent advances in predicting and modeling protein-protein interactions. Trends Biochem Sci 2023; 48:527-538. [PMID: 37061423 DOI: 10.1016/j.tibs.2023.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 04/17/2023]
Abstract
Protein-protein interactions (PPIs) drive biological processes, and disruption of PPIs can cause disease. With recent breakthroughs in structure prediction and a deluge of genomic sequence data, computational methods to predict PPIs and model spatial structures of protein complexes are now approaching the accuracy of experimental approaches for permanent interactions and show promise for elucidating transient interactions. As we describe here, the key to this success is rich evolutionary information deciphered from thousands of homologous sequences that coevolve in interacting partners. This covariation signal, revealed by sophisticated statistical and machine learning (ML) algorithms, predicts physiological interactions. Accurate artificial intelligence (AI)-based modeling of protein structures promises to provide accurate 3D models of PPIs at a proteome-wide scale.
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Affiliation(s)
- Jesse Durham
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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30
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Huang Y, Wuchty S, Zhou Y, Zhang Z. SGPPI: structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network. Brief Bioinform 2023; 24:6995378. [PMID: 36682013 DOI: 10.1093/bib/bbad020] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/17/2022] [Accepted: 01/05/2023] [Indexed: 01/23/2023] Open
Abstract
While deep learning (DL)-based models have emerged as powerful approaches to predict protein-protein interactions (PPIs), the reliance on explicit similarity measures (e.g. sequence similarity and network neighborhood) to known interacting proteins makes these methods ineffective in dealing with novel proteins. The advent of AlphaFold2 presents a significant opportunity and also a challenge to predict PPIs in a straightforward way based on monomer structures while controlling bias from protein sequences. In this work, we established Structure and Graph-based Predictions of Protein Interactions (SGPPI), a structure-based DL framework for predicting PPIs, using the graph convolutional network. In particular, SGPPI focused on protein patches on the protein-protein binding interfaces and extracted the structural, geometric and evolutionary features from the residue contact map to predict PPIs. We demonstrated that our model outperforms traditional machine learning methods and state-of-the-art DL-based methods using non-representation-bias benchmark datasets. Moreover, our model trained on human dataset can be reliably transferred to predict yeast PPIs, indicating that SGPPI can capture converging structural features of protein interactions across various species. The implementation of SGPPI is available at https://github.com/emerson106/SGPPI.
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Affiliation(s)
- Yan Huang
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Department of Biomedical Informatics, Ministry of Education Key Laboratory of Molecular Cardiovascular Sciences, Center for Non-Coding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
- Institute of Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
| | - Yuan Zhou
- Department of Biomedical Informatics, Ministry of Education Key Laboratory of Molecular Cardiovascular Sciences, Center for Non-Coding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Ziding Zhang
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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31
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Chen S, Liang C, Li H, Yu W, Prothiwa M, Kopczynski D, Loroch S, Fransen M, Verhelst SHL. Pepstatin-Based Probes for Photoaffinity Labeling of Aspartic Proteases and Application to Target Identification. ACS Chem Biol 2023; 18:686-692. [PMID: 36920024 DOI: 10.1021/acschembio.2c00946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Aspartic proteases are a small class of proteases implicated in a wide variety of human diseases. Covalent chemical probes for photoaffinity labeling (PAL) of these proteases are underdeveloped. We here report a full on-resin synthesis of clickable PAL probes based on the natural product inhibitor pepstatin incorporating a minimal diazirine reactive group. The position of this group in the inhibitor determines the labeling efficiency. The most effective probes sensitively detect cathepsin D, a biomarker for breast cancer, in cell lysates. Moreover, through chemical proteomics experiments and deep learning algorithms, we identified sequestosome-1, an important player in autophagy, as a direct interaction partner and substrate of cathepsin D.
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Affiliation(s)
- Suyuan Chen
- Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Chunguang Liang
- Bioinformatik, Biozentrum, Universität Würzburg, 97074 Würzburg, Germany.,Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Hongli Li
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Peroxisome Biology and Intracellular Communication, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Weimeng Yu
- Bioinformatik, Biozentrum, Universität Würzburg, 97074 Würzburg, Germany
| | - Michaela Prothiwa
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Stefan Loroch
- Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Ruhr-Universität Bochum, Medizinisches Proteom-Center, Building ProDi E2.240, Gesundheitscampus 4, D-44801 Bochum, Germany.,ProtiFi LLC, 1000 Turk Hill Road, Suite 180, 2nd Floor, Fairport, New York 14450, United States
| | - Marc Fransen
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Peroxisome Biology and Intracellular Communication, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Steven H L Verhelst
- Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49 box 901b, 3000 Leuven, Belgium
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32
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Kibar G, Vingron M. Prediction of protein-protein interactions using sequences of intrinsically disordered regions. Proteins 2023. [PMID: 36908253 DOI: 10.1002/prot.26486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
Protein-protein interactions (PPIs) play a crucial role in numerous molecular processes. Despite many efforts, mechanisms governing molecular recognition between interacting proteins remain poorly understood and it is particularly challenging to predict from sequence whether two proteins can interact. Here we present a new method to tackle this challenge using intrinsically disordered regions (IDRs). IDRs are protein segments that are functional despite lacking a single invariant three-dimensional structure. The prevalence of IDRs in eukaryotic proteins suggests that IDRs are critical for interactions. To test this hypothesis, we predicted PPIs using IDR sequences in candidate proteins in humans. Moreover, we divide the PPI prediction problem into two specific subproblems and adapt appropriate training and test strategies based on problem type. Our findings underline the importance of defining clearly the problem type and show that sequences encoding IDRs can aid in predicting specific features of the protein interaction network of intrinsically disordered proteins. Our findings further suggest that accounting for IDRs in future analyses should accelerate efforts to elucidate the eukaryotic PPI network.
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Affiliation(s)
- Gözde Kibar
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
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33
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Petrey D, Zhao H, Trudeau S, Murray D, Honig B. PrePPI: A structure informed proteome-wide database of protein-protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530276. [PMID: 36909476 PMCID: PMC10002632 DOI: 10.1101/2023.02.27.530276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
We present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural clues within a Bayesian framework to compute a likelihood ratio (LR) for essentially every possible pair of proteins in a proteome; the current database is for the human interactome. The structural modeling (SM) clue is derived from templatebased modeling and its application on a proteome-wide scale is enabled by a unique scoring function used to evaluate a putative complex. The updated version of PrePPI leverages AlphaFold structures that are parsed into individual domains. As has been demonstrated in earlier applications, PrePPI performs extremely well as measured by receiver operating characteristic curves derived from testing on E. coli and human protein-protein interaction (PPI) databases. A PrePPI database of ~1.3 million human PPIs can be queried with a webserver application that comprises multiple functionalities for examining query proteins, template complexes, 3D models for predicted complexes, and related features ( https://honiglab.c2b2.columbia.edu/PrePPI ). PrePPI is a state-of- the-art resource that offers an unprecedented structure-informed view of the human interactome. Graphic Abstract
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34
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A graph neural network model for deciphering the biological mechanisms of plant electrical signal classification. Appl Soft Comput 2023. [DOI: 10.1016/j.asoc.2023.110153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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35
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Soleymani F, Paquet E, Viktor HL, Michalowski W, Spinello D. ProtInteract: A deep learning framework for predicting protein-protein interactions. Comput Struct Biotechnol J 2023; 21:1324-1348. [PMID: 36817951 PMCID: PMC9929211 DOI: 10.1016/j.csbj.2023.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Proteins mainly perform their functions by interacting with other proteins. Protein-protein interactions underpin various biological activities such as metabolic cycles, signal transduction, and immune response. However, due to the sheer number of proteins, experimental methods for finding interacting and non-interacting protein pairs are time-consuming and costly. We therefore developed the ProtInteract framework to predict protein-protein interaction. ProtInteract comprises two components: first, a novel autoencoder architecture that encodes each protein's primary structure to a lower-dimensional vector while preserving its underlying sequence attributes. This leads to faster training of the second network, a deep convolutional neural network (CNN) that receives encoded proteins and predicts their interaction under three different scenarios. In each scenario, the deep CNN predicts the class of a given encoded protein pair. Each class indicates different ranges of confidence scores corresponding to the probability of whether a predicted interaction occurs or not. The proposed framework features significantly low computational complexity and relatively fast response. The contributions of this work are twofold. First, ProtInteract assimilates the protein's primary structure into a pseudo-time series. Therefore, we leverage the nature of the time series of proteins and their physicochemical properties to encode a protein's amino acid sequence into a lower-dimensional vector space. This approach enables extracting highly informative sequence attributes while reducing computational complexity. Second, the ProtInteract framework utilises this information to identify protein interactions with other proteins based on its amino acid configuration. Our results suggest that the proposed framework performs with high accuracy and efficiency in predicting protein-protein interactions.
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Affiliation(s)
- Farzan Soleymani
- Department of Mechanical Engineering, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Eric Paquet
- National Research Council, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada,Corresponding author.
| | - Herna Lydia Viktor
- School of Electrical Engineering and Computer Science, University of Ottawa, ON K1N 6N5, Canada
| | | | - Davide Spinello
- Department of Mechanical Engineering, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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36
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Rogers JR, Nikolényi G, AlQuraishi M. Growing ecosystem of deep learning methods for modeling protein-protein interactions. Protein Eng Des Sel 2023; 36:gzad023. [PMID: 38102755 DOI: 10.1093/protein/gzad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
Numerous cellular functions rely on protein-protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep learning has emerged as a promising approach for tackling this problem by exploiting both experimental data and basic biophysical knowledge about protein interactions. Here, we review the growing ecosystem of deep learning methods for modeling protein interactions, highlighting the diversity of these biophysically informed models and their respective trade-offs. We discuss recent successes in using representation learning to capture complex features pertinent to predicting protein interactions and interaction sites, geometric deep learning to reason over protein structures and predict complex structures, and generative modeling to design de novo protein assemblies. We also outline some of the outstanding challenges and promising new directions. Opportunities abound to discover novel interactions, elucidate their physical mechanisms, and engineer binders to modulate their functions using deep learning and, ultimately, unravel how protein interactions orchestrate complex cellular behaviors.
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Affiliation(s)
- Julia R Rogers
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Gergő Nikolényi
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
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Ortiz-Vilchis P, De-la-Cruz-García JS, Ramirez-Arellano A. Identification of Relevant Protein Interactions with Partial Knowledge: A Complex Network and Deep Learning Approach. BIOLOGY 2023; 12:140. [PMID: 36671832 PMCID: PMC9856098 DOI: 10.3390/biology12010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023]
Abstract
Protein-protein interactions (PPIs) are the basis for understanding most cellular events in biological systems. Several experimental methods, e.g., biochemical, molecular, and genetic methods, have been used to identify protein-protein associations. However, some of them, such as mass spectrometry, are time-consuming and expensive. Machine learning (ML) techniques have been widely used to characterize PPIs, increasing the number of proteins analyzed simultaneously and optimizing time and resources for identifying and predicting protein-protein functional linkages. Previous ML approaches have focused on well-known networks or specific targets but not on identifying relevant proteins with partial or null knowledge of the interaction networks. The proposed approach aims to generate a relevant protein sequence based on bidirectional Long-Short Term Memory (LSTM) with partial knowledge of interactions. The general framework comprises conducting a scale-free and fractal complex network analysis. The outcome of these analyses is then used to fine-tune the fractal method for the vital protein extraction of PPI networks. The results show that several PPI networks are self-similar or fractal, but that both features cannot coexist. The generated protein sequences (by the bidirectional LSTM) also contain an average of 39.5% of proteins in the original sequence. The average length of the generated sequences was 17% of the original one. Finally, 95% of the generated sequences were true.
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Affiliation(s)
- Pilar Ortiz-Vilchis
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Jazmin-Susana De-la-Cruz-García
- Sección de Estudios de Posgrado e Investigación, Unidad Profesional Interdisciplinaria de Ingeniería y Ciencias Sociales y Administrativas, Instituto Politécnico Nacional, Mexico City 08400, Mexico
| | - Aldo Ramirez-Arellano
- Sección de Estudios de Posgrado e Investigación, Unidad Profesional Interdisciplinaria de Ingeniería y Ciencias Sociales y Administrativas, Instituto Politécnico Nacional, Mexico City 08400, Mexico
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Murakami Y, Mizuguchi K. Recent developments of sequence-based prediction of protein-protein interactions. Biophys Rev 2022; 14:1393-1411. [PMID: 36589735 PMCID: PMC9789376 DOI: 10.1007/s12551-022-01038-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
The identification of protein-protein interactions (PPIs) can lead to a better understanding of cellular functions and biological processes of proteins and contribute to the design of drugs to target disease-causing PPIs. In addition, targeting host-pathogen PPIs is useful for elucidating infection mechanisms. Although several experimental methods have been used to identify PPIs, these methods can yet to draw complete PPI networks. Hence, computational techniques are increasingly required for the prediction of potential PPIs, which have never been seen experimentally. Recent high-performance sequence-based methods have contributed to the construction of PPI networks and the elucidation of pathogenetic mechanisms in specific diseases. However, the usefulness of these methods depends on the quality and quantity of training data of PPIs. In this brief review, we introduce currently available PPI databases and recent sequence-based methods for predicting PPIs. Also, we discuss key issues in this field and present future perspectives of the sequence-based PPI predictions.
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Affiliation(s)
- Yoichi Murakami
- grid.440890.10000 0004 0640 9413Tokyo University of Information Sciences, 4-1 Onaridai, Wakaba-Ku, Chiba, 265-8501 Japan
| | - Kenji Mizuguchi
- grid.136593.b0000 0004 0373 3971Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-Shi, Osaka, 565-0871 Japan ,grid.482562.fNational Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085 Japan
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Huang Y, Zhang Z, Zhou Y. AbAgIntPre: A deep learning method for predicting antibody-antigen interactions based on sequence information. Front Immunol 2022; 13:1053617. [PMID: 36618397 PMCID: PMC9813736 DOI: 10.3389/fimmu.2022.1053617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Antibody-mediated immunity is an essential part of the immune system in vertebrates. The ability to specifically bind to antigens allows antibodies to be widely used in the therapy of cancers and other critical diseases. A key step in antibody therapeutics is the experimental identification of antibody-antigen interactions, which is generally time-consuming, costly, and laborious. Although some computational methods have been proposed to screen potential antibodies, the dependence on 3D structures still limits the application of these methods. Methods Here, we developed a deep learning-assisted prediction method (i.e., AbAgIntPre) for fast identification of antibody-antigen interactions that only relies on amino acid sequences. A Siamese-like convolutional neural network architecture was established with the amino acid composition encoding scheme for both antigens and antibodies. Results and Discussion The generic model of AbAgIntPre achieved satisfactory performance with the Area Under Curve (AUC) of 0.82 on a high-quality generic independent test dataset. Besides, this approach also showed competitive performance on the more specific SARS-CoV dataset. We expect that AbAgIntPre can serve as an important complement to traditional experimental methods for antibody screening and effectively reduce the workload of antibody design. The web server of AbAgIntPre is freely available at http://www.zzdlab.com/AbAgIntPre.
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Affiliation(s)
- Yan Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China,Department of Biomedical Informatics, Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China,*Correspondence: Ziding Zhang, ; Yuan Zhou,
| | - Yuan Zhou
- Department of Biomedical Informatics, Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, School of Basic Medical Sciences, Peking University, Beijing, China,*Correspondence: Ziding Zhang, ; Yuan Zhou,
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Yang X, Zheng Y, Xing X, Sui X, Jia W, Pan H. Immune subtype identification and multi-layer perceptron classifier construction for breast cancer. Front Oncol 2022; 12:943874. [PMID: 36568197 PMCID: PMC9780074 DOI: 10.3389/fonc.2022.943874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Breast cancer is a heterogeneous tumor. Tumor microenvironment (TME) has an important effect on the proliferation, metastasis, treatment, and prognosis of breast cancer. Methods In this study, we calculated the relative proportion of tumor infiltrating immune cells (TIICs) in the breast cancer TME, and used the consensus clustering algorithm to cluster the breast cancer subtypes. We also developed a multi-layer perceptron (MLP) classifier based on a deep learning framework to detect breast cancer subtypes, which 70% of the breast cancer research cohort was used for the model training and 30% for validation. Results By performing the K-means clustering algorithm, the research cohort was clustered into two subtypes. The Kaplan-Meier survival estimate analysis showed significant differences in the overall survival (OS) between the two identified subtypes. Estimating the difference in the relative proportion of TIICs showed that the two subtypes had significant differences in multiple immune cells, such as CD8, CD4, and regulatory T cells. Further, the expression level of immune checkpoint molecules (PDL1, CTLA4, LAG3, TIGIT, CD27, IDO1, ICOS) and tumor mutational burden (TMB) also showed significant differences between the two subtypes, indicating the clinical value of the two subtypes. Finally, we identified a 38-gene signature and developed a multilayer perceptron (MLP) classifier that combined multi-gene signature to identify breast cancer subtypes. The results showed that the classifier had an accuracy rate of 93.56% and can be robustly used for the breast cancer subtype diagnosis. Conclusion Identification of breast cancer subtypes based on the immune signature in the tumor microenvironment can assist clinicians to effectively and accurately assess the progression of breast cancer and formulate different treatment strategies for different subtypes.
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Affiliation(s)
- Xinbo Yang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Yuanjie Zheng
- School of Information Science and Engineering, Shandong Normal University, Jinan, China,*Correspondence: Yuanjie Zheng, ; Huali Pan,
| | - Xianrong Xing
- Department of Pharmacy, Shandong Medical College, Jinan, China
| | - Xiaodan Sui
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Weikuan Jia
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Huali Pan
- School of Information Science and Engineering, Shandong Normal University, Jinan, China,Business School, Shandong Normal University, Jinan, China,*Correspondence: Yuanjie Zheng, ; Huali Pan,
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Koca MB, Nourani E, Abbasoğlu F, Karadeniz İ, Sevilgen FE. Graph convolutional network based virus-human protein-protein interaction prediction for novel viruses. Comput Biol Chem 2022; 101:107755. [PMID: 36037723 DOI: 10.1016/j.compbiolchem.2022.107755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/07/2022] [Accepted: 08/10/2022] [Indexed: 11/03/2022]
Abstract
Computational identification of human-virus protein-protein interactions (PHIs) is a worthwhile step towards understanding infection mechanisms. Analysis of the PHI networks is important for the determination of pathogenic diseases. Prediction of these interactions is a popular problem since experimental detection of PHIs is both time-consuming and expensive. The available methods use biological features like amino acid sequences, molecular structure, or biological activities for prediction. Recent studies show that the topological properties of proteins in protein-protein interaction (PPI) networks increase the performance of the predictions. The basic network projections, random-walk-based models, or graph neural networks are used for generating topologically enriched (hybrid) protein embeddings. In this study, we propose a three-stage machine learning pipeline that generates and uses hybrid embeddings for PHI prediction. In the first stage, numerical features are extracted from the amino acid sequences using the Doc2Vec and Byte Pair Encoding method. The amino acid embeddings are used as node features while training a modified GraphSAGE model, which is an improved version of the graph convolutional network. Lastly, the hybrid protein embeddings are used for training a binary interaction classifier model that predicts whether there is an interaction between the given two proteins or not. The proposed method is evaluated with comprehensive experiments to test its functionality and compare it with the state-of-art methods. The experimental results on the benchmark dataset prove the efficiency of the proposed model by having a 3-23% better area under curve (AUC) score than its competitors.
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Affiliation(s)
- Mehmet Burak Koca
- Department of Computer Engineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkey
| | - Esmaeil Nourani
- Department of Information Technology, Faculty of Computer Engineering and Information Technology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Ferda Abbasoğlu
- Department of Computer Engineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkey
| | - İlknur Karadeniz
- Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Işık University, İstanbul, Turkey.
| | - Fatih Erdoğan Sevilgen
- Department of Computer Engineering, Faculty of Engineering, Gebze Technical University, Kocaeli, Turkey; Institute for Data Science and Artificial Intelligence, Boğaziçi University, İstanbul, Turkey
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42
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Bernhofer M, Rost B. TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinformatics 2022; 23:326. [PMID: 35941534 PMCID: PMC9358067 DOI: 10.1186/s12859-022-04873-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4-5 times underrepresented compared to non-TMPs. Today's top methods such as AlphaFold2 accurately predict 3D structures for many TMPs, but annotating transmembrane regions remains a limiting step for proteome-wide predictions. RESULTS Here, we present TMbed, a novel method inputting embeddings from protein Language Models (pLMs, here ProtT5), to predict for each residue one of four classes: transmembrane helix (TMH), transmembrane strand (TMB), signal peptide, or other. TMbed completes predictions for entire proteomes within hours on a single consumer-grade desktop machine at performance levels similar or better than methods, which are using evolutionary information from multiple sequence alignments (MSAs) of protein families. On the per-protein level, TMbed correctly identified 94 ± 8% of the beta barrel TMPs (53 of 57) and 98 ± 1% of the alpha helical TMPs (557 of 571) in a non-redundant data set, at false positive rates well below 1% (erred on 30 of 5654 non-membrane proteins). On the per-segment level, TMbed correctly placed, on average, 9 of 10 transmembrane segments within five residues of the experimental observation. Our method can handle sequences of up to 4200 residues on standard graphics cards used in desktop PCs (e.g., NVIDIA GeForce RTX 3060). CONCLUSIONS Based on embeddings from pLMs and two novel filters (Gaussian and Viterbi), TMbed predicts alpha helical and beta barrel TMPs at least as accurately as any other method but at lower false positive rates. Given the few false positives and its outstanding speed, TMbed might be ideal to sieve through millions of 3D structures soon to be predicted, e.g., by AlphaFold2.
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Affiliation(s)
- Michael Bernhofer
- Department of Informatics, Bioinformatics and Computational Biology ‑ i12, Technical University of Munich (TUM), Boltzmannstr. 3, 85748, Garching, Germany.
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany.
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology ‑ i12, Technical University of Munich (TUM), Boltzmannstr. 3, 85748, Garching, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching, Germany
- TUM School of Life Sciences Weihenstephan (TUM-WZW), Alte Akademie 8, Freising, Germany
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43
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Bell EW, Schwartz JH, Freddolino PL, Zhang Y. PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. J Mol Biol 2022; 434:167530. [PMID: 35662463 PMCID: PMC8897833 DOI: 10.1016/j.jmb.2022.167530] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 03/03/2022] [Indexed: 01/31/2023]
Abstract
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of non-interactions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.
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Affiliation(s)
- Eric W Bell
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jacob H Schwartz
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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Harmalkar A, Mahajan SP, Gray JJ. Induced fit with replica exchange improves protein complex structure prediction. PLoS Comput Biol 2022; 18:e1010124. [PMID: 35658008 PMCID: PMC9200320 DOI: 10.1371/journal.pcbi.1010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/15/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Despite the progress in prediction of protein complexes over the last decade, recent blind protein complex structure prediction challenges revealed limited success rates (less than 20% models with DockQ score > 0.4) on targets that exhibit significant conformational change upon binding. To overcome limitations in capturing backbone motions, we developed a new, aggressive sampling method that incorporates temperature replica exchange Monte Carlo (T-REMC) and conformational sampling techniques within docking protocols in Rosetta. Our method, ReplicaDock 2.0, mimics induced-fit mechanism of protein binding to sample backbone motions across putative interface residues on-the-fly, thereby recapitulating binding-partner induced conformational changes. Furthermore, ReplicaDock 2.0 clocks in at 150-500 CPU hours per target (protein-size dependent); a runtime that is significantly faster than Molecular Dynamics based approaches. For a benchmark set of 88 proteins with moderate to high flexibility (unbound-to-bound iRMSD over 1.2 Å), ReplicaDock 2.0 successfully docks 61% of moderately flexible complexes and 35% of highly flexible complexes. Additionally, we demonstrate that by biasing backbone sampling particularly towards residues comprising flexible loops or hinge domains, highly flexible targets can be predicted to under 2 Å accuracy. This indicates that additional gains are possible when mobile protein segments are known.
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Affiliation(s)
- Ameya Harmalkar
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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46
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Casadio R, Martelli PL, Savojardo C. Machine learning solutions for predicting protein–protein interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rita Casadio
- Biocomputing Group University of Bologna Bologna Italy
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47
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Abstract
Summary Computational methods to predict protein–protein interaction (PPI) typically segregate into sequence-based ‘bottom-up’ methods that infer properties from the characteristics of the individual protein sequences, or global ‘top-down’ methods that infer properties from the pattern of already known PPIs in the species of interest. However, a way to incorporate top-down insights into sequence-based bottom-up PPI prediction methods has been elusive. We thus introduce Topsy-Turvy, a method that newly synthesizes both views in a sequence-based, multi-scale, deep-learning model for PPI prediction. While Topsy-Turvy makes predictions using only sequence data, during the training phase it takes a transfer-learning approach by incorporating patterns from both global and molecular-level views of protein interaction. In a cross-species context, we show it achieves state-of-the-art performance, offering the ability to perform genome-scale, interpretable PPI prediction for non-model organisms with no existing experimental PPI data. In species with available experimental PPI data, we further present a Topsy-Turvy hybrid (TT-Hybrid) model which integrates Topsy-Turvy with a purely network-based model for link prediction that provides information about species-specific network rewiring. TT-Hybrid makes accurate predictions for both well- and sparsely-characterized proteins, outperforming both its constituent components as well as other state-of-the-art PPI prediction methods. Furthermore, running Topsy-Turvy and TT-Hybrid screens is feasible for whole genomes, and thus these methods scale to settings where other methods (e.g. AlphaFold-Multimer) might be infeasible. The generalizability, accuracy and genome-level scalability of Topsy-Turvy and TT-Hybrid unlocks a more comprehensive map of protein interaction and organization in both model and non-model organisms. Availability and implementation https://topsyturvy.csail.mit.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Samuel Sledzieski
- Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bonnie Berger
- To whom correspondence should be addressed. E-mail: or
| | - Lenore Cowen
- To whom correspondence should be addressed. E-mail: or
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48
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Hu X, Feng C, Ling T, Chen M. Deep learning frameworks for protein–protein interaction prediction. Comput Struct Biotechnol J 2022; 20:3223-3233. [PMID: 35832624 PMCID: PMC9249595 DOI: 10.1016/j.csbj.2022.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/27/2022] [Accepted: 06/12/2022] [Indexed: 11/26/2022] Open
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Abstract
Motivation Protein functions are often described using the Gene Ontology (GO) which is an ontology consisting of over 50 000 classes and a large set of formal axioms. Predicting the functions of proteins is one of the key challenges in computational biology and a variety of machine learning methods have been developed for this purpose. However, these methods usually require a significant amount of training data and cannot make predictions for GO classes that have only few or no experimental annotations. Results We developed DeepGOZero, a machine learning model which improves predictions for functions with no or only a small number of annotations. To achieve this goal, we rely on a model-theoretic approach for learning ontology embeddings and combine it with neural networks for protein function prediction. DeepGOZero can exploit formal axioms in the GO to make zero-shot predictions, i.e., predict protein functions even if not a single protein in the training phase was associated with that function. Furthermore, the zero-shot prediction method employed by DeepGOZero is generic and can be applied whenever associations with ontology classes need to be predicted. Availability and implementation http://github.com/bio-ontology-research-group/deepgozero. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maxat Kulmanov
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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