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Biswas G, Mukherjee D, Dutta N, Ghosh P, Basu S. EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations. J Mol Model 2023; 29:239. [PMID: 37423912 DOI: 10.1007/s00894-023-05626-0] [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: 03/23/2023] [Accepted: 06/20/2023] [Indexed: 07/11/2023]
Abstract
CONTEXT Protein-protein interaction (PPI) is a key component linked to virtually all cellular processes. Be it an enzyme catalysis ('classic type functions' of proteins) or a signal transduction ('non-classic'), proteins generally function involving stable or quasi-stable multi-protein associations. The physical basis for such associations is inherent in the combined effect of shape and electrostatic complementarities (Sc, EC) of the interacting protein partners at their interface, which provides indirect probabilistic estimates of the stability and affinity of the interaction. While Sc is a necessary criterion for inter-protein associations, EC can be favorable as well as disfavored (e.g., in transient interactions). Estimating equilibrium thermodynamic parameters (∆Gbinding, Kd) by experimental means is costly and time consuming, thereby opening windows for computational structural interventions. Attempts to empirically probe ∆Gbinding from coarse-grain structural descriptors (primarily, surface area based terms) have lately been overtaken by physics-based, knowledge-based and their hybrid approaches (MM/PBSA, FoldX, etc.) that directly compute ∆Gbinding without involving intermediate structural descriptors. METHODS Here, we present EnCPdock ( https://www.scinetmol.in/EnCPdock/ ), a user-friendly web-interface for the direct conjoint comparative analyses of complementarity and binding energetics in proteins. EnCPdock returns an AI-predicted ∆Gbinding computed by combining complementarity (Sc, EC) and other high-level structural descriptors (input feature vectors), and renders a prediction accuracy comparable to the state-of-the-art. EnCPdock further locates a PPI complex in terms of its {Sc, EC} values (taken as an ordered pair) in the two-dimensional complementarity plot (CP). In addition, it also generates mobile molecular graphics of the interfacial atomic contact network for further analyses. EnCPdock also furnishes individual feature trends along with the relative probability estimates (Prfmax) of the obtained feature-scores with respect to the events of their highest observed frequencies. Together, these functionalities are of real practical use for structural tinkering and intervention as might be relevant in the design of targeted protein-interfaces. Combining all its features and applications, EnCPdock presents a unique online tool that should be beneficial to structural biologists and researchers across related fraternities.
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Affiliation(s)
- Gargi Biswas
- Department of Chemistry and Structural Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Debasish Mukherjee
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Nalok Dutta
- Dept of Biochemical Engineering, Faculty of Engineering Science, University College London, London, WC1E 6BT, UK
| | - Prithwi Ghosh
- Department of Botany, Narajole Raj College, Vidyasagar University, Midnapore, 721211, India
| | - Sankar Basu
- Department of Microbiology, Asutosh College (affiliated with University of Calcutta), 92, Shyama Prasad Mukherjee Rd, Bhowanipore, 700026, Kolkata, India.
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2
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Wells NGM, Smith CA. Predicting binding affinity changes from long-distance mutations using molecular dynamics simulations and Rosetta. Proteins 2023. [PMID: 36757060 DOI: 10.1002/prot.26477] [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: 10/13/2022] [Revised: 01/20/2023] [Accepted: 02/07/2023] [Indexed: 02/10/2023]
Abstract
Computationally modeling how mutations affect protein-protein binding not only helps uncover the biophysics of protein interfaces, but also enables the redesign and optimization of protein interactions. Traditional high-throughput methods for estimating binding free energy changes are currently limited to mutations directly at the interface due to difficulties in accurately modeling how long-distance mutations propagate their effects through the protein structure. However, the modeling and design of such mutations is of substantial interest as it allows for greater control and flexibility in protein design applications. We have developed a method that combines high-throughput Rosetta-based side-chain optimization with conformational sampling using classical molecular dynamics simulations, finding significant improvements in our ability to accurately predict long-distance mutational perturbations to protein binding. Our approach uses an analytical framework grounded in alchemical free energy calculations while enabling exploration of a vastly larger sequence space. When comparing to experimental data, we find that our method can predict internal long-distance mutational perturbations with a level of accuracy similar to that of traditional methods in predicting the effects of mutations at the protein-protein interface. This work represents a new and generalizable approach to optimize protein free energy landscapes for desired biological functions.
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Affiliation(s)
- Nicholas G M Wells
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
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Liu J, Xia KL, Wu J, Yau SST, Wei GW. Biomolecular Topology: Modelling and Analysis. ACTA MATHEMATICA SINICA, ENGLISH SERIES 2022; 38:1901-1938. [PMID: 36407804 PMCID: PMC9640850 DOI: 10.1007/s10114-022-2326-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/12/2022] [Indexed: 05/25/2023]
Abstract
With the great advancement of experimental tools, a tremendous amount of biomolecular data has been generated and accumulated in various databases. The high dimensionality, structural complexity, the nonlinearity, and entanglements of biomolecular data, ranging from DNA knots, RNA secondary structures, protein folding configurations, chromosomes, DNA origami, molecular assembly, to others at the macromolecular level, pose a severe challenge in their analysis and characterization. In the past few decades, mathematical concepts, models, algorithms, and tools from algebraic topology, combinatorial topology, computational topology, and topological data analysis, have demonstrated great power and begun to play an essential role in tackling the biomolecular data challenge. In this work, we introduce biomolecular topology, which concerns the topological problems and models originated from the biomolecular systems. More specifically, the biomolecular topology encompasses topological structures, properties and relations that are emerged from biomolecular structures, dynamics, interactions, and functions. We discuss the various types of biomolecular topology from structures (of proteins, DNAs, and RNAs), protein folding, and protein assembly. A brief discussion of databanks (and databases), theoretical models, and computational algorithms, is presented. Further, we systematically review related topological models, including graphs, simplicial complexes, persistent homology, persistent Laplacians, de Rham-Hodge theory, Yau-Hausdorff distance, and the topology-based machine learning models.
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Affiliation(s)
- Jian Liu
- School of Mathematical Sciences, Hebei Normal University, Shijiazhuang, 050024 P. R. China
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, 101408 P. R. China
| | - Ke-Lin Xia
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 639798 Singapore
| | - Jie Wu
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, 101408 P. R. China
- Department of Mathematical Sciences, Tsinghua University, Beijing, 100084 P. R. China
| | - Stephen Shing-Toung Yau
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, 101408 P. R. China
- Department of Mathematical Sciences, Tsinghua University, Beijing, 100084 P. R. China
| | - Guo-Wei Wei
- Department of Mathematics & Department of Biochemistry and Molecular Biology & Department of Electrical and Computer Engineering, Michigan State University, Wells Hall 619 Red Cedar Road, East Lansing, MI 48824-1027 USA
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4
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Liu X, Feng H, Wu J, Xia K. Hom-Complex-Based Machine Learning (HCML) for the Prediction of Protein-Protein Binding Affinity Changes upon Mutation. J Chem Inf Model 2022; 62:3961-3969. [PMID: 36040839 DOI: 10.1021/acs.jcim.2c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions (PPIs) are involved in almost all biological processes in the cell. Understanding protein-protein interactions holds the key for the understanding of biological functions, diseases and the development of therapeutics. Recently, artificial intelligence (AI) models have demonstrated great power in PPIs. However, a key issue for all AI-based PPI models is efficient molecular representations and featurization. Here, we propose Hom-complex-based PPI representation, and Hom-complex-based machine learning models for the prediction of PPI binding affinity changes upon mutation, for the first time. In our model, various Hom complexes Hom(G1, G) can be generated for the graph representation G of protein-protein complex by using different graphs G1, which reveal G1-related inner connections within the graph representation G of protein-protein complex. Further, for a specific graph G1, a series of nested Hom complexes are generated to give a multiscale characterization of the PPIs. Its persistent homology and persistent Euler characteristic are used as molecular descriptors and further combined with the machine learning model, in particular, gradient boosting tree (GBT). We systematically test our model on the two most-commonly used data sets, that is, SKEMPI and AB-Bind. It has been found that our model outperforms all the existing models as far as we know, which demonstrates the great potential of our model for the analysis of PPIs. Our model can be used for the analysis and design of efficient antibodies for SARS-CoV-2.
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Affiliation(s)
- Xiang Liu
- Chern Institute of Mathematics and LPMC, Nankai University, Tianjin, China, 300071.,Division of Mathematical Sciences, School of Physical and Mathematical Sciences Nanyang Technological University, Singapore 637371
| | - Huitao Feng
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences Nanyang Technological University, Singapore 637371.,Mathematical Science Research Center, Chongqing University of Technology, Chongqing, China, 400054
| | - Jie Wu
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications (BIMSA), Beijing, China,101408
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences Nanyang Technological University, Singapore 637371
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5
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Wee J, Xia K. Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction. Brief Bioinform 2022; 23:6533501. [PMID: 35189639 DOI: 10.1093/bib/bbac024] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) play a significant role in nearly all cellular and biological activities. Data-driven machine learning models have demonstrated great power in PPIs. However, the design of efficient molecular featurization poses a great challenge for all learning models for PPIs. Here, we propose persistent spectral (PerSpect) based PPI representation and featurization, and PerSpect-based ensemble learning (PerSpect-EL) models for PPI binding affinity prediction, for the first time. In our model, a sequence of Hodge (or combinatorial) Laplacian (HL) matrices at various different scales are generated from a specially designed filtration process. PerSpect attributes, which are statistical and combinatorial properties of spectrum information from these HL matrices, are used as features for PPI characterization. Each PerSpect attribute is input into a 1D convolutional neural network (CNN), and these CNN networks are stacked together in our PerSpect-based ensemble learning models. We systematically test our model on the two most commonly used datasets, i.e. SKEMPI and AB-Bind. It has been found that our model can achieve state-of-the-art results and outperform all existing models to the best of our knowledge.
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Affiliation(s)
- JunJie Wee
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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6
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Chen YC, Chen YH, Wright JD, Lim C. PPI-Hotspot DB: Database of Protein-Protein Interaction Hot Spots. J Chem Inf Model 2022; 62:1052-1060. [PMID: 35147037 DOI: 10.1021/acs.jcim.2c00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single-point mutations of certain residues (so-called hot spots) impair/disrupt protein-protein interactions (PPIs), leading to pathogenesis and drug resistance. Conventionally, a PPI-hot spot is identified when its replacement decreased the binding free energy significantly, generally by ≥2 kcal/mol. The relatively few mutations with such a significant binding free energy drop limited the number of distinct PPI-hot spots. By defining PPI-hot spots based on mutations that have been manually curated in UniProtKB to significantly impair/disrupt PPIs in addition to binding free energy changes, we have greatly expanded the number of distinct PPI-hot spots by an order of magnitude. These experimentally determined PPI-hot spots along with available structures have been collected in a database called PPI-HotspotDB. We have applied the PPI-HotspotDB to create a nonredundant benchmark, PPI-Hotspot+PDBBM, for assessing methods to predict PPI-hot spots using the free structure as input. PPI-HotspotDB will benefit the design of mutagenesis experiments and development of PPI-hot spot prediction methods. The database and benchmark are freely available at https://ppihotspot.limlab.dnsalias.org.
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Affiliation(s)
- Yao Chi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsien Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Jon D Wright
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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7
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Xiong D, Lee D, Li L, Zhao Q, Yu H. Implications of disease-related mutations at protein-protein interfaces. Curr Opin Struct Biol 2022; 72:219-225. [PMID: 34959033 PMCID: PMC8863207 DOI: 10.1016/j.sbi.2021.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/01/2021] [Accepted: 11/18/2021] [Indexed: 02/03/2023]
Abstract
Protein-protein interfaces have been attracting great attention owing to their critical roles in protein-protein interactions and the fact that human disease-related mutations are generally enriched in them. Recently, substantial research progress has been made in this field, which has significantly promoted the understanding and treatment of various human diseases. For example, many studies have discovered the properties of disease-related mutations. Besides, as more large-scale experimental data become available, various computational approaches have been proposed to advance our understanding of disease mutations from the data. Here, we overview recent advances in characteristics of disease-related mutations at protein-protein interfaces, mutation effects on protein interactions, and investigation of mutations on specific diseases.
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Affiliation(s)
- Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dongjin Lee
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Le Li
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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8
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Chen C, Boorla VS, Banerjee D, Chowdhury R, Cavener VS, Nissly RH, Gontu A, Boyle NR, Vandegrift K, Nair MS, Kuchipudi SV, Maranas CD. Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2. Proc Natl Acad Sci U S A 2021; 118:e2106480118. [PMID: 34588290 PMCID: PMC8594574 DOI: 10.1073/pnas.2106480118] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 01/22/2023] Open
Abstract
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single-amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single- and multiple-amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.
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Affiliation(s)
- Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Deepro Banerjee
- The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Victoria S Cavener
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Nina R Boyle
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Kurt Vandegrift
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802;
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802;
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9
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Amengual-Rigo P, Fernández-Recio J, Guallar V. UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. Bioinformatics 2021; 37:334-341. [PMID: 32761082 DOI: 10.1093/bioinformatics/btaa708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Single protein residue mutations may reshape the binding affinity of protein-protein interactions. Therefore, predicting its effects is of great interest in biotechnology and biomedicine. Unfortunately, the availability of experimental data on binding affinity changes upon mutation is limited, which hampers the development of new and more precise algorithms. Here, we propose UEP, a classifier for predicting beneficial and detrimental mutations in protein-protein complexes trained on interactome data. RESULTS Regardless of the simplicity of the UEP algorithm, which is based on a simple three-body contact potential derived from interactome data, we report competitive results with the gold standard methods in this field with the advantage of being faster in terms of computational time. Moreover, we propose a consensus selection procedure by involving the combination of three predictors that showed higher classification accuracy in our benchmark: UEP, pyDock and EvoEF1/FoldX. Overall, we demonstrate that the analysis of interactome data allows predicting the impact of protein-protein mutations using UEP, a fast and reliable open-source code. AVAILABILITY AND IMPLEMENTATION UEP algorithm can be found at: https://github.com/pepamengual/UEP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pep Amengual-Rigo
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Juan Fernández-Recio
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de la Rioja-Gobierno de la Rioja, 26007 Logroño, Spain
| | - Victor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,ICREA: Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
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10
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Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure 2021; 29:606-621.e5. [PMID: 33539768 DOI: 10.1016/j.str.2021.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 11/15/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023]
Abstract
Accurate predictive modeling of antibody-antigen complex structures and structure-based antibody design remain major challenges in computational biology, with implications for biotherapeutics, immunity, and vaccines. Through a systematic search for high-resolution structures of antibody-antigen complexes and unbound antibody and antigen structures, in conjunction with identification of experimentally determined binding affinities, we have assembled a non-redundant set of test cases for antibody-antigen docking and affinity prediction. This benchmark more than doubles the number of antibody-antigen complexes and corresponding affinities available in our previous benchmarks, providing an unprecedented view of the determinants of antibody recognition and insights into molecular flexibility. Initial assessments of docking and affinity prediction tools highlight the challenges posed by this diverse set of cases, which includes camelid nanobodies, therapeutic monoclonal antibodies, and broadly neutralizing antibodies targeting viral glycoproteins. This dataset will enable development of advanced predictive modeling and design methods for this therapeutically relevant class of protein-protein interactions.
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Affiliation(s)
- Johnathan D Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jing Zhou
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Iain Moal
- Computational Sciences, GlaxoSmithKline Research and Development, Stevenage SG1 2NY, UK
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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11
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Shringari SR, Giannakoulias S, Ferrie JJ, Petersson EJ. Rosetta custom score functions accurately predict ΔΔG of mutations at protein-protein interfaces using machine learning. Chem Commun (Camb) 2020; 56:6774-6777. [PMID: 32441721 DOI: 10.1039/d0cc01959c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein-protein interfaces play essential roles in a variety of biological processes and many therapeutic molecules are targeted at these interfaces. However, accurate predictions of the effects of interfacial mutations to identify "hotspots" have remained elusive despite the myriad of modeling and machine learning methods tested. Here, for the first time, we demonstrate that nonlinear reweighting of energy terms from Rosetta, through the use of machine learning, exhibits improved predictability of ΔΔG values associated with interfacial mutations.
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Affiliation(s)
- Sumant R Shringari
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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12
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Pahari S, Li G, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E. SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions. Int J Mol Sci 2020; 21:E2563. [PMID: 32272725 PMCID: PMC7177817 DOI: 10.3390/ijms21072563] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/26/2022] Open
Abstract
Maintaining wild type protein-protein interactions is essential for the normal function of cell and any mutation that alter their characteristics can cause disease. Therefore, the ability to correctly and quickly predict the effect of amino acid mutations is crucial for understanding disease effects and to be able to carry out genome-wide studies. Here, we report a new development of the SAAMBE method, SAAMBE-3D, which is a machine learning-based approach, resulting in accurate predictions and is extremely fast. It achieves the Pearson correlation coefficient ranging from 0.78 to 0.82 depending on the training protocol in benchmarking five-fold validation test against the SKEMPI v2.0 database and outperforms currently existing algorithms on various blind-tests. Furthermore, optimized and tested via five-fold cross-validation on the Cornell University dataset, the SAAMBE-3D achieves AUC of 1.0 and 0.96 on a homo and hereto-dimer test datasets. Another important feature of SAAMBE-3D is that it is very fast, it takes less than a fraction of a second to complete a prediction. SAAMBE-3D is available as a web server and as well as a stand-alone code, the last one being another important feature allowing other researchers to directly download the code and run it on their local computer. Combined all together, SAAMBE-3D is an accurate and fast software applicable for genome-wide studies to assess the effect of amino acid mutations on protein-protein interactions. The webserver and the stand-alone codes (SAAMBE-3D for predicting the change of binding free energy and SAAMBE-3D-DN for predicting if the mutation is disruptive or non-disruptive) are available.
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Affiliation(s)
- Swagata Pahari
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
| | - Gen Li
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
| | - Adithya Krishna Murthy
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA; (S.L.); (R.F.); (H.Y.)
| | - Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA; (S.L.); (R.F.); (H.Y.)
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA; (S.L.); (R.F.); (H.Y.)
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (S.P.); (G.L.); (A.K.M.)
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Generating quantitative binding landscapes through fractional binding selections combined with deep sequencing and data normalization. Nat Commun 2020; 11:297. [PMID: 31941882 PMCID: PMC6962383 DOI: 10.1038/s41467-019-13895-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/28/2019] [Indexed: 11/09/2022] Open
Abstract
Quantifying the effects of various mutations on binding free energy is crucial for understanding the evolution of protein-protein interactions and would greatly facilitate protein engineering studies. Yet, measuring changes in binding free energy (ΔΔGbind) remains a tedious task that requires expression of each mutant, its purification, and affinity measurements. We developed an attractive approach that allows us to quantify ΔΔGbind for thousands of protein mutants in one experiment. Our protocol combines protein randomization, Yeast Surface Display technology, deep sequencing, and a few experimental ΔΔGbind data points on purified proteins to generate ΔΔGbind values for the remaining numerous mutants of the same protein complex. Using this methodology, we comprehensively map the single-mutant binding landscape of one of the highest-affinity interaction between BPTI and Bovine Trypsin (BT). We show that ΔΔGbind for this interaction could be quantified with high accuracy over the range of 12 kcal mol−1 displayed by various BPTI single mutants. Quantifying the effect of mutations on binding free energy is important to understand protein-protein interaction (PPI). Here the authors develop a method based on yeast display and next-generation sequencing to generate quantitative binding landscapes for any PPI regardless of their Kd value.
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14
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Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics 2019; 35:462-469. [PMID: 30020414 PMCID: PMC6361233 DOI: 10.1093/bioinformatics/bty635] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/17/2018] [Indexed: 11/18/2022] Open
Abstract
Motivation Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the assembly and regulation of molecular complexes, the mechanisms through which mutations lead to disease, and protein engineering. Results We present SKEMPI 2.0, a major update to our database of binding free energy changes upon mutation for structurally resolved protein–protein interactions. This version now contains manually curated binding data for 7085 mutations, an increase of 133%, including changes in kinetics for 1844 mutations, enthalpy and entropy changes for 443 mutations, and 440 mutations, which abolish detectable binding. Availability and implementation The database is available as supplementary data and at https://life.bsc.es/pid/skempi2/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justina Jankauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Brian Jiménez-García
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Justas Dapkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institut de Biologia Molecular de Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Iain H Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
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15
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Cong Q, Anishchenko I, Ovchinnikov S, Baker D. Protein interaction networks revealed by proteome coevolution. SCIENCE (NEW YORK, N.Y.) 2019; 365:185-189. [PMID: 31296772 DOI: 10.1126/science.aaw6718] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/07/2019] [Indexed: 01/19/2023]
Abstract
Residue-residue coevolution has been observed across a number of protein-protein interfaces, but the extent of residue coevolution between protein families on the whole-proteome scale has not been systematically studied. We investigate coevolution between 5.4 million pairs of proteins in Escherichia coli and between 3.9 millions pairs in Mycobacterium tuberculosis We find strong coevolution for binary complexes involved in metabolism and weaker coevolution for larger complexes playing roles in genetic information processing. We take advantage of this coevolution, in combination with structure modeling, to predict protein-protein interactions (PPIs) with an accuracy that benchmark studies suggest is considerably higher than that of proteome-wide two-hybrid and mass spectrometry screens. We identify hundreds of previously uncharacterized PPIs in E. coli and M. tuberculosis that both add components to known protein complexes and networks and establish the existence of new ones.
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Affiliation(s)
- Qian Cong
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA. .,Institute for Protein Design, University of Washington, Seattle, WA 98105, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
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16
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Geng C, Xue LC, Roel‐Touris J, Bonvin AMJJ. Finding the ΔΔ
G
spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1410] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cunliang Geng
- Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry Utrecht University Utrecht The Netherlands
| | - Li C. Xue
- Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry Utrecht University Utrecht The Netherlands
| | - Jorge Roel‐Touris
- Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry Utrecht University Utrecht The Netherlands
| | - Alexandre M. J. J. Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry Utrecht University Utrecht The Netherlands
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17
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Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B 2018; 122:5389-5399. [PMID: 29401388 DOI: 10.1021/acs.jpcb.7b11367] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Computationally modeling changes in binding free energies upon mutation (interface ΔΔ G) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticity should be able to achieve higher prediction accuracy over methods that do not. To test this hypothesis, we developed a method within the Rosetta macromolecular modeling suite (flex ddG) that samples conformational diversity using "backrub" to generate an ensemble of models and then applies torsion minimization, side chain repacking, and averaging across this ensemble to estimate interface ΔΔ G values. We tested our method on a curated benchmark set of 1240 mutants, and found the method outperformed existing methods that sampled conformational space to a lesser degree. We observed considerable improvements with flex ddG over existing methods on the subset of small side chain to large side chain mutations, as well as for multiple simultaneous non-alanine mutations, stabilizing mutations, and mutations in antibody-antigen interfaces. Finally, we applied a generalized additive model (GAM) approach to the Rosetta energy function; the resulting nonlinear reweighting model improved the agreement with experimentally determined interface ΔΔ G values but also highlighted the necessity of future energy function improvements.
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Affiliation(s)
- Kyle A Barlow
- Graduate Program in Bioinformatics , University of California San Francisco , San Francisco , California , United States of America
| | - Shane Ó Conchúir
- California Institute for Quantitative Biosciences , University of California San Francisco , San Francisco , California , United States of America.,Department of Bioengineering and Therapeutic Sciences , University of California San Francisco , San Francisco , California , United States of America
| | - Samuel Thompson
- Graduate Program in Biophysics , University of California San Francisco , San Francisco , California , United States of America
| | - Pooja Suresh
- Graduate Program in Biophysics , University of California San Francisco , San Francisco , California , United States of America
| | - James E Lucas
- Graduate Program in Bioengineering , University of California San Francisco , San Francisco , California , United States of America
| | - Markus Heinonen
- Department of Computer Science , Aalto University , Espoo , Finland.,Helsinki Institute for Information Technology (HIIT) , Helsinki , Finland
| | - Tanja Kortemme
- Graduate Program in Bioinformatics , University of California San Francisco , San Francisco , California , United States of America.,California Institute for Quantitative Biosciences , University of California San Francisco , San Francisco , California , United States of America.,Department of Bioengineering and Therapeutic Sciences , University of California San Francisco , San Francisco , California , United States of America.,Graduate Program in Biophysics , University of California San Francisco , San Francisco , California , United States of America.,Graduate Program in Bioengineering , University of California San Francisco , San Francisco , California , United States of America.,Chan Zuckerberg Biohub , San Francisco , California 94158 , United States
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18
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Goodacre N, Edwards N, Danielsen M, Uetz P, Wu C. Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017; 14:1082-1093. [PMID: 26812731 DOI: 10.1109/tcbb.2016.2520931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The human genome contains a large number of protein polymorphisms due to individual genome variation. How many of these polymorphisms lead to altered protein-protein interaction is unknown. We have developed a method to address this question. The intersection of the SKEMPI database (of affinity constants among interacting proteins) and CAPRI 4.0 docking benchmark was docked using HADDOCK, leading to a training set of 166 mutant pairs. A random forest classifier based on the differences in resulting docking scores between the 166 mutant pairs and their wild-types was used, to distinguish between variants that have either completely or partially lost binding ability. Fifty percent of non-binders were correctly predicted with a false discovery rate of only 2 percent. The model was tested on a set of 15 HIV-1 - human, as well as seven human- human glioblastoma-related, mutant protein pairs: 50 percent of combined non-binders were correctly predicted with a false discovery rate of 10 percent. The model was also used to identify 10 protein-protein interactions between human proteins and their HIV-1 partners that are likely to be abolished by rare non-synonymous single-nucleotide polymorphisms (nsSNPs). These nsSNPs may represent novel and potentially therapeutically-valuable targets for anti-viral therapy by disruption of viral binding.
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19
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Moal IH, Barradas-Bautista D, Jiménez-García B, Torchala M, van der Velde A, Vreven T, Weng Z, Bates PA, Fernández-Recio J. IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. Bioinformatics 2017; 33:1806-1813. [PMID: 28200016 PMCID: PMC5783285 DOI: 10.1093/bioinformatics/btx068] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/26/2017] [Accepted: 02/12/2017] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. RESULTS Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. AVAILABILITY AND IMPLEMENTATION IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request. CONTACT moal@ebi.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Iain H Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Didier Barradas-Bautista
- Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Brian Jiménez-García
- Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Arjan van der Velde
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Juan Fernández-Recio
- Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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20
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Geng C, Vangone A, Bonvin AMJJ. Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes. Protein Eng Des Sel 2016; 29:291-299. [PMID: 27284087 DOI: 10.1093/protein/gzw020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 11/14/2022] Open
Abstract
Reliable prediction of binding affinity changes (ΔΔG) upon mutations in protein complexes relies not only on the performance of computational methods but also on the availability and quality of experimental data. Binding affinity changes can be measured by various experimental methods with different accuracies and limitations. To understand the impact of these on the prediction of binding affinity change, we present the Database of binding Affinity Change Upon Mutation (DACUM), a database of 1872 binding affinity changes upon single-point mutations, a subset of the SKEMPI database (Moal,I.H. and Fernández-Recio,J. Bioinformatics, 2012;28:2600-2607) extended with information on the experimental methods used for ΔΔG measurements. The ΔΔG data were classified into different data sets based on the experimental method used and the position of the mutation (interface and non-interface). We tested the prediction performance of the original HADDOCK score, a newly trained version of it and mutation Cutoff Scanning Matrix (Pires,D.E.V., Ascher,D.B. and Blundell,T.L. Bioinformatics 2014;30:335-342), one of the best reported ΔΔG predictors so far, on these various data sets. Our results demonstrate a strong impact of the experimental methods on the performance of binding affinity change predictors for protein complexes. This underscores the importance of properly considering and carefully choosing experimental methods in the development of novel binding affinity change predictors. The DACUM database is available online at https://github.com/haddocking/DACUM.
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Affiliation(s)
- Cunliang Geng
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Anna Vangone
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
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21
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Brender JR, Zhang Y. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. PLoS Comput Biol 2015; 11:e1004494. [PMID: 26506533 PMCID: PMC4624718 DOI: 10.1371/journal.pcbi.1004494] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/06/2015] [Indexed: 11/18/2022] Open
Abstract
The formation of protein-protein complexes is essential for proteins to perform their physiological functions in the cell. Mutations that prevent the proper formation of the correct complexes can have serious consequences for the associated cellular processes. Since experimental determination of protein-protein binding affinity remains difficult when performed on a large scale, computational methods for predicting the consequences of mutations on binding affinity are highly desirable. We show that a scoring function based on interface structure profiles collected from analogous protein-protein interactions in the PDB is a powerful predictor of protein binding affinity changes upon mutation. As a standalone feature, the differences between the interface profile score of the mutant and wild-type proteins has an accuracy equivalent to the best all-atom potentials, despite being two orders of magnitude faster once the profile has been constructed. Due to its unique sensitivity in collecting the evolutionary profiles of analogous binding interactions and the high speed of calculation, the interface profile score has additional advantages as a complementary feature to combine with physics-based potentials for improving the accuracy of composite scoring approaches. By incorporating the sequence-derived and residue-level coarse-grained potentials with the interface structure profile score, a composite model was constructed through the random forest training, which generates a Pearson correlation coefficient >0.8 between the predicted and observed binding free-energy changes upon mutation. This accuracy is comparable to, or outperforms in most cases, the current best methods, but does not require high-resolution full-atomic models of the mutant structures. The binding interface profiling approach should find useful application in human-disease mutation recognition and protein interface design studies. Few proteins carry out their tasks in isolation. Instead, proteins combine with each other in complicated ways that can be affected by either the natural genetic variation that occurs among people or by disease causing mutations such as those that occur in cancer or in genetic disorders. To understand how these mutations affect our health, it is necessary to understand how mutations can affect the strength of the interactions that bind proteins together. This is a difficult task to do in a laboratory on a large scale and scientists are increasingly turning to computational methods to predict these effects in advance. We show that by looking at the multiple alignments of similar protein-protein complex structures at the interface regions, new constraints based on the evolution of the three dimensional structures of proteins can be made to predict which mutations are compatible with two proteins interacting and which are not.
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Affiliation(s)
- Jeffrey R. Brender
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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22
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Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AMJJ, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol 2015; 427:3031-41. [PMID: 26231283 PMCID: PMC4677049 DOI: 10.1016/j.jmb.2015.07.016] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/31/2023]
Abstract
We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein-protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r=0.52 overall and r=0.72 for the rigid complexes.
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Affiliation(s)
- Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Iain H Moal
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
| | - Anna Vangone
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Brian G Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom
| | - Raphael Chaleil
- Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom
| | - Brian Jiménez-García
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom.
| | - Juan Fernandez-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain.
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands.
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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23
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Moal IH, Dapkūnas J, Fernández-Recio J. Inferring the microscopic surface energy of protein-protein interfaces from mutation data. Proteins 2015; 83:640-50. [PMID: 25586563 DOI: 10.1002/prot.24761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/04/2014] [Accepted: 12/21/2014] [Indexed: 11/11/2022]
Abstract
Mutations at protein-protein recognition sites alter binding strength by altering the chemical nature of the interacting surfaces. We present a simple surface energy model, parameterized with empirical ΔΔG values, yielding mean energies of -48 cal mol(-1) Å(-2) for interactions between hydrophobic surfaces, -51 to -80 cal mol(-1) Å(-2) for surfaces of complementary charge, and 66-83 cal mol(-1) Å(-2) for electrostatically repelling surfaces, relative to the aqueous phase. This places the mean energy of hydrophobic surface burial at -24 cal mol(-1) Å(-2) . Despite neglecting configurational entropy and intramolecular changes, the model correlates with empirical binding free energies of a functionally diverse set of rigid-body interactions (r = 0.66). When used to rerank docking poses, it can place near-native solutions in the top 10 for 37% of the complexes evaluated, and 82% in the top 100. The method shows that hydrophobic burial is the driving force for protein association, accounting for 50-95% of the cohesive energy. The model is available open-source from http://life.bsc.es/pid/web/surface_energy/ and via the CCharpPPI web server http://life.bsc.es/pid/ccharppi/.
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Affiliation(s)
- Iain H Moal
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, Barcelona, 08034, Spain
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24
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Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-Protein Interactions: Structures and Druggability. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Moal IH, Jiménez-García B, Fernández-Recio J. CCharPPI web server: computational characterization of protein-protein interactions from structure. Bioinformatics 2014; 31:123-5. [PMID: 25183488 DOI: 10.1093/bioinformatics/btu594] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
SUMMARY The atomic structures of protein-protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions. AVAILABILITY AND IMPLEMENTATION The server does not require registration by the user and is freely available for non-commercial academic use at http://life.bsc.es/pid/ccharppi.
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Affiliation(s)
- Iain H Moal
- Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
| | - Brian Jiménez-García
- Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
| | - Juan Fernández-Recio
- Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
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26
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Dourado DFAR, Flores SC. A multiscale approach to predicting affinity changes in protein-protein interfaces. Proteins 2014; 82:2681-90. [PMID: 24975440 DOI: 10.1002/prot.24634] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/12/2014] [Accepted: 06/18/2014] [Indexed: 11/07/2022]
Abstract
Substitution mutations in protein-protein interfaces can have a substantial effect on binding, which has consequences in basic and applied biomedical research. Experimental expression, purification, and affinity determination of protein complexes is an expensive and time-consuming means of evaluating the effect of mutations, making a fast and accurate in silico method highly desirable. When the structure of the wild-type complex is known, it is possible to economically evaluate the effect of point mutations with knowledge based potentials, which do not model backbone flexibility, but these have been validated only for single mutants. Substitution mutations tend to induce local conformational rearrangements only. Accordingly, ZEMu (Zone Equilibration of Mutants) flexibilizes only a small region around the site of mutation, then computes its dynamics under a physics-based force field. We validate with 1254 experimental mutants (with 1-15 simultaneous substitutions) in a wide variety of different protein environments (65 protein complexes), and obtain a significant improvement in the accuracy of predicted ΔΔG.
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Affiliation(s)
- Daniel F A R Dourado
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University, 751 24, Uppsala, Sweden
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Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Proteins 2013; 81:2192-200. [PMID: 23934865 DOI: 10.1002/prot.24387] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/06/2022]
Abstract
In addition to protein-protein docking, this CAPRI edition included new challenges, like protein-water and protein-sugar interactions, or the prediction of binding affinities and ΔΔG changes upon mutation. Regarding the standard protein-protein docking cases, our approach, mostly based on the pyDock scheme, submitted correct models as predictors and as scorers for 67% and 57% of the evaluated targets, respectively. In this edition, available information on known interface residues hardly made any difference for our predictions. In one of the targets, the inclusion of available experimental small-angle X-ray scattering (SAXS) data using our pyDockSAXS approach slightly improved the predictions. In addition to the standard protein-protein docking assessment, new challenges were proposed. One of the new problems was predicting the position of the interface water molecules, for which we submitted models with 20% and 43% of the water-mediated native contacts predicted as predictors and scorers, respectively. Another new problem was the prediction of protein-carbohydrate binding, where our submitted model was very close to being acceptable. A set of targets were related to the prediction of binding affinities, in which our pyDock scheme was able to discriminate between natural and designed complexes with area under the curve = 83%. It was also proposed to estimate the effect of point mutations on binding affinity. Our approach, based on machine learning methods, showed high rates of correctly classified mutations for all cases. The overall results were highly rewarding, and show that the field is ready to move forward and face new interesting challenges in interactomics.
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Affiliation(s)
- Chiara Pallara
- Joint BSC-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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Moal IH, Torchala M, Bates PA, Fernández-Recio J. The scoring of poses in protein-protein docking: current capabilities and future directions. BMC Bioinformatics 2013; 14:286. [PMID: 24079540 PMCID: PMC3850738 DOI: 10.1186/1471-2105-14-286] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/25/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ranking of docked poses using a scoring function, for which many methods have been developed. There is a need to explore the differences and commonalities of these methods with each other, as well as with functions developed in the fields of molecular dynamics and homology modelling. RESULTS We present an evaluation of 115 scoring functions on an unbound docking decoy benchmark covering 118 complexes for which a near-native solution can be found, yielding top 10 success rates of up to 58%. Hierarchical clustering is performed, so as to group together functions which identify near-natives in similar subsets of complexes. Three set theoretic approaches are used to identify pairs of scoring functions capable of correctly scoring different complexes. This shows that functions in different clusters capture different aspects of binding and are likely to work together synergistically. CONCLUSIONS All functions designed specifically for docking perform well, indicating that functions are transferable between sampling methods. We also identify promising methods from the field of homology modelling. Further, differential success rates by docking difficulty and solution quality suggest a need for flexibility-dependent scoring. Investigating pairs of scoring functions, the set theoretic measures identify known scoring strategies as well as a number of novel approaches, indicating promising augmentations of traditional scoring methods. Such augmentation and parameter combination strategies are discussed in the context of the learning-to-rank paradigm.
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Affiliation(s)
- Iain H Moal
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Super computing Center, Barcelona 08034, Spain
| | - Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | - Juan Fernández-Recio
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Super computing Center, Barcelona 08034, Spain
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Moal IH, Moretti R, Baker D, Fernández-Recio J. Scoring functions for protein-protein interactions. Curr Opin Struct Biol 2013; 23:862-7. [PMID: 23871100 DOI: 10.1016/j.sbi.2013.06.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 06/26/2013] [Accepted: 06/29/2013] [Indexed: 12/24/2022]
Abstract
The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been developed to quantify the structural and energetic properties of interacting proteins, finding use in interrelated challenges revolving around the relationship between sequence, structure and binding free energy. These include loop modelling, side-chain refinement, docking, multimer assembly, affinity prediction, affinity change upon mutation, hotspots location and interface design. Information derived from models optimised for one of these challenges can be used to benefit the others, and can be unified within the theoretical frameworks of multi-task learning and Pareto-optimal multi-objective learning.
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Affiliation(s)
- Iain H Moal
- Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, C/ Jordi Girona 29, 08034 Barcelona, Spain
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