Computational prediction of protein-protein interactions

Microbiome modeling: a beginner's guide

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.

A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions

Protein functions are characterized by interactions with proteins, drugs, and other biomolecules. Understanding these interactions is essential for deciphering the molecular mechanisms underlying biological processes and developing new therapeutic strategies. Current computational methods mostly predict interactions based on either molecular network or structural information, without integrating them within a unified multi-scale framework. While a few multi-view learning methods are devoted to fusing the multi-scale information, these methods tend to rely intensively on a single scale and under-fitting the others, likely attributed to the imbalanced nature and inherent greediness of multi-scale learning. To alleviate the optimization imbalance, we present MUSE, a multi-scale representation learning framework based on a variant expectation maximization to optimize different scales in an alternating procedure over multiple iterations. This strategy efficiently fuses multi-scale information between atomic structure and molecular network scale through mutual supervision and iterative optimization. MUSE outperforms the current state-of-the-art models not only in molecular interaction (protein-protein, drug-protein, and drug-drug) tasks but also in protein interface prediction at the atomic structure scale. More importantly, the multi-scale learning framework shows potential for extension to other scales of computational drug discovery.

In Silico Analysis of Protein-Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe

Ermp1 is a putative metalloprotease from Schizosaccharomyces pombe and a member of the Fxna peptidases. Although their function is unknown, orthologous proteins from rats and humans have been associated with the maturation of ovarian follicles and increased ER stress. This study focuses on proposing the first prediction of PPI by comparison of the interologues between humans and yeasts, as well as the molecular docking and dynamics of the M28 domain of Ermp1 with possible target proteins. As results, 45 proteins are proposed that could interact with the metalloprotease. Most of these proteins are related to the transport of Ca2+ and the metabolism of amino acids and proteins. Docking and molecular dynamics suggest that the M28 domain of Ermp1 could hydrolyze leucine and methionine residues of Amk2, Ypt5 and Pex12. These results could support future experimental investigations of other Fxna peptidases, such as human ERMP1.

Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments

Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.

Repurposing approved non-oncology drugs for cancer therapy: a comprehensive review of mechanisms, efficacy, and clinical prospects

Cancer poses a significant global health challenge, with predictions of increasing prevalence in the coming years due to limited prevention, late diagnosis, and inadequate success with current therapies. In addition, the high cost of new anti-cancer drugs creates barriers in meeting the medical needs of cancer patients, especially in developing countries. The lengthy and costly process of developing novel drugs further hinders drug discovery and clinical implementation. Therefore, there has been a growing interest in repurposing approved drugs for other diseases to address the urgent need for effective cancer treatments. The aim of this comprehensive review is to provide an overview of the potential of approved non-oncology drugs as therapeutic options for cancer treatment. These drugs come from various chemotherapeutic classes, including antimalarials, antibiotics, antivirals, anti-inflammatory drugs, and antifungals, and have demonstrated significant antiproliferative, pro-apoptotic, immunomodulatory, and antimetastatic properties. A systematic review of the literature was conducted to identify relevant studies on the repurposing of approved non-oncology drugs for cancer therapy. Various electronic databases, such as PubMed, Scopus, and Google Scholar, were searched using appropriate keywords. Studies focusing on the therapeutic potential, mechanisms of action, efficacy, and clinical prospects of repurposed drugs in cancer treatment were included in the analysis. The review highlights the promising outcomes of repurposing approved non-oncology drugs for cancer therapy. Drugs belonging to different therapeutic classes have demonstrated notable antitumor effects, including inhibiting cell proliferation, promoting apoptosis, modulating the immune response, and suppressing metastasis. These findings suggest the potential of these repurposed drugs as effective therapeutic approaches in cancer treatment. Repurposing approved non-oncology drugs provides a promising strategy for addressing the urgent need for effective and accessible cancer treatments. The diverse classes of repurposed drugs, with their demonstrated antiproliferative, pro-apoptotic, immunomodulatory, and antimetastatic properties, offer new avenues for cancer therapy. Further research and clinical trials are warranted to explore the full potential of these repurposed drugs and optimize their use in treating various cancer types. Repurposing approved drugs can significantly expedite the process of identifying effective treatments and improve patient outcomes in a cost-effective manner.

Network Analytics Enabled by Generating a Pool of Network Variants from Noisy Data

Mapping network nodes and edges to communities and network functions is crucial to gaining a higher level of understanding of the network structure and functions. Such mappings are particularly challenging to design for covert social networks, which intentionally hide their structure and functions to protect important members from attacks or arrests. Here, we focus on correctly inferring the structures and functions of such networks, but our methodology can be broadly applied. Without the ground truth, knowledge about the allocation of nodes to communities and network functions, no single network based on the noisy data can represent all plausible communities and functions of the true underlying network. To address this limitation, we apply a generative model that randomly distorts the original network based on the noisy data, generating a pool of statistically equivalent networks. Each unique generated network is recorded, while each duplicate of the already recorded network just increases the repetition count of that network. We treat each such network as a variant of the ground truth with the probability of arising in the real world approximated by the ratio of the count of this network's duplicates plus one to the total number of all generated networks. Communities of variants with frequently occurring duplicates contain persistent patterns shared by their structures. Using Shannon entropy, we can find a variant that minimizes the uncertainty for operations planned on the network. Repeatedly generating new pools of networks from the best network of the previous step for several steps lowers the entropy of the best new variant. If the entropy is too high, the network operators can identify nodes, the monitoring of which can achieve the most significant reduction in entropy. Finally, we also present a heuristic for constructing a new variant, which is not randomly generated but has the lowest expected cost of operating on the distorted mappings of network nodes to communities and functions caused by noisy data.

Electrostatic complementarity at the interface drives transient protein-protein interactions

Understanding the mechanisms driving bio-molecules binding and determining the resulting complexes' stability is fundamental for the prediction of binding regions, which is the starting point for drug-ability and design. Characteristics like the preferentially hydrophobic composition of the binding interfaces, the role of van der Waals interactions, and the consequent shape complementarity between the interacting molecular surfaces are well established. However, no consensus has yet been reached on the role of electrostatic. Here, we perform extensive analyses on a large dataset of protein complexes for which both experimental binding affinity and pH data were available. Probing the amino acid composition, the disposition of the charges, and the electrostatic potential they generated on the protein molecular surfaces, we found that (i) although different classes of dimers do not present marked differences in the amino acid composition and charges disposition in the binding region, (ii) homodimers with identical binding region show higher electrostatic compatibility with respect to both homodimers with non-identical binding region and heterodimers. Interestingly, (iii) shape and electrostatic complementarity, for patches defined on short-range interactions, behave oppositely when one stratifies the complexes by their binding affinity: complexes with higher binding affinity present high values of shape complementarity (the role of the Lennard-Jones potential predominates) while electrostatic tends to be randomly distributed. Conversely, complexes with low values of binding affinity exploit Coulombic complementarity to acquire specificity, suggesting that electrostatic complementarity may play a greater role in transient (or less stable) complexes. In light of these results, (iv) we provide a novel, fast, and efficient method, based on the 2D Zernike polynomial formalism, to measure electrostatic complementarity without the need of knowing the complex structure. Expanding the electrostatic potential on a basis of 2D orthogonal polynomials, we can discriminate between transient and permanent protein complexes with an AUC of the ROC of [Formula: see text] 0.8. Ultimately, our work helps shedding light on the non-trivial relationship between the hydrophobic and electrostatic contributions in the binding interfaces, thus favoring the development of new predictive methods for binding affinity characterization.

Deep learning-assisted prediction of protein-protein interactions in Arabidopsis thaliana

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.

Graph-BERT and language model-based framework for protein-protein interaction identification

Identification of protein-protein interactions (PPI) is among the critical problems in the domain of bioinformatics. Previous studies have utilized different AI-based models for PPI classification with advances in artificial intelligence (AI) techniques. The input to these models is the features extracted from different sources of protein information, mainly sequence-derived features. In this work, we present an AI-based PPI identification model utilizing a PPI network and protein sequences. The PPI network is represented as a graph where each node is a protein pair, and an edge is defined between two nodes if there exists a common protein between these nodes. Each node in a graph has a feature vector. In this work, we have used the language model to extract feature vectors directly from protein sequences. The feature vectors for protein in pairs are concatenated and used as a node feature vector of a PPI network graph. Finally, we have used the Graph-BERT model to encode the PPI network graph with sequence-based features and learn the hidden representation of the feature vector for each node. The next step involves feeding the learned representations of nodes to the fully connected layer, the output of which is fed into the softmax layer to classify the protein interactions. To assess the efficacy of the proposed PPI model, we have performed experiments on several PPI datasets. The experimental results demonstrate that the proposed approach surpasses the existing PPI works and designed baselines in classifying PPI.

SGPPI: structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network

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.

Hierarchical graph learning for protein-protein interaction

Protein-Protein Interactions (PPIs) are fundamental means of functions and signalings in biological systems. The massive growth in demand and cost associated with experimental PPI studies calls for computational tools for automated prediction and understanding of PPIs. Despite recent progress, in silico methods remain inadequate in modeling the natural PPI hierarchy. Here we present a double-viewed hierarchical graph learning model, HIGH-PPI, to predict PPIs and extrapolate the molecular details involved. In this model, we create a hierarchical graph, in which a node in the PPI network (top outside-of-protein view) is a protein graph (bottom inside-of-protein view). In the bottom view, a group of chemically relevant descriptors, instead of the protein sequences, are used to better capture the structure-function relationship of the protein. HIGH-PPI examines both outside-of-protein and inside-of-protein of the human interactome to establish a robust machine understanding of PPIs. This model demonstrates high accuracy and robustness in predicting PPIs. Moreover, HIGH-PPI can interpret the modes of action of PPIs by identifying important binding and catalytic sites precisely. Overall, "HIGH-PPI [ https://github.com/zqgao22/HIGH-PPI ]" is a domain-knowledge-driven and interpretable framework for PPI prediction studies.

Application of machine learning on understanding biomolecule interactions in cellular machinery

Machine learning (ML) applications have become ubiquitous in all fields of research including protein science and engineering. Apart from protein structure and mutation prediction, scientists are focusing on knowledge gaps with respect to the molecular mechanisms involved in protein binding and interactions with other components in the experimental setups or the human body. Researchers are working on several wet-lab techniques and generating data for a better understanding of concepts and mechanics involved. The information like biomolecular structure, binding affinities, structure fluctuations and movements are enormous which can be handled and analyzed by ML. Therefore, this review highlights the significance of ML in understanding the biomolecular interactions while assisting in various fields of research such as drug discovery, nanomedicine, nanotoxicity and material science. Hence, the way ahead would be to force hand-in hand of laboratory work and computational techniques.

ProtInteract: A deep learning framework for predicting protein-protein interactions

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.

Cytotrap: An Innovative Approach for Protein-Protein Interaction Studies for Cytoplasmic Proteins

Protein-protein interaction mapping has gained immense importance in understanding protein functions in diverse biological pathways. There are various in vivo and in vitro techniques associated with the protein-protein interaction studies but generally, the focus is confined to understanding the protein interaction in the nucleus of the cell, and thus it limits the availability to explore protein interactions that are happening in the cytoplasm of the cell. Since posttranslational modification is a crucial step in signaling pathways and cellular protein interactions harnessing the cytoplasmic protein and evaluating the interaction in the cytoplasm, this protocol will provide more information about studying these types of protein interactions. Cytotrap is a type of yeast-two-hybrid system that differs in its ability to anchor along the membrane, thus directing the protein of interest to anchor along the membrane through the myristoylation signaling unit. The vector containing the target protein contains the myristoylation unit, called the prey, and the bait unit contains the protein of interest as a fusion with the hSos protein. In an event of interaction between the target and the protein of interest, the hSos protein unit will be localized to the membrane and the GDP/GTP exchange unit will trigger the activation of the Ras pathway that leads to the survival of the temperature-sensitive yeast strain at a higher temperature.

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest

Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scattered across different database resources, experimental modalities and levels of mechanistic detail. The STRING database (https://string-db.org/) systematically collects and integrates protein-protein interactions-both physical interactions as well as functional associations. The data originate from a number of sources: automated text mining of the scientific literature, computational interaction predictions from co-expression, conserved genomic context, databases of interaction experiments and known complexes/pathways from curated sources. All of these interactions are critically assessed, scored, and subsequently automatically transferred to less well-studied organisms using hierarchical orthology information. The data can be accessed via the website, but also programmatically and via bulk downloads. The most recent developments in STRING (version 12.0) are: (i) it is now possible to create, browse and analyze a full interaction network for any novel genome of interest, by submitting its complement of encoded proteins, (ii) the co-expression channel now uses variational auto-encoders to predict interactions, and it covers two new sources, single-cell RNA-seq and experimental proteomics data and (iii) the confidence in each experimentally derived interaction is now estimated based on the detection method used, and communicated to the user in the web-interface. Furthermore, STRING continues to enhance its facilities for functional enrichment analysis, which are now fully available also for user-submitted genomes.

Protein-protein interaction prediction with deep learning: A comprehensive review

Most proteins perform their biological function by interacting with themselves or other molecules. Thus, one may obtain biological insights into protein functions, disease prevalence, and therapy development by identifying protein-protein interactions (PPI). However, finding the interacting and non-interacting protein pairs through experimental approaches is labour-intensive and time-consuming, owing to the variety of proteins. Hence, protein-protein interaction and protein-ligand binding problems have drawn attention in the fields of bioinformatics and computer-aided drug discovery. Deep learning methods paved the way for scientists to predict the 3-D structure of proteins from genomes, predict the functions and attributes of a protein, and modify and design new proteins to provide desired functions. This review focuses on recent deep learning methods applied to problems including predicting protein functions, protein-protein interaction and their sites, protein-ligand binding, and protein design.

Graph Neural Network for Protein-Protein Interaction Prediction: A Comparative Study

Proteins are the fundamental biological macromolecules which underline practically all biological activities. Protein-protein interactions (PPIs), as they are known, are how proteins interact with other proteins in their environment to perform biological functions. Understanding PPIs reveals how cells behave and operate, such as the antigen recognition and signal transduction in the immune system. In the past decades, many computational methods have been developed to predict PPIs automatically, requiring less time and resources than experimental techniques. In this paper, we present a comparative study of various graph neural networks for protein-protein interaction prediction. Five network models are analyzed and compared, including neural networks (NN), graph convolutional neural networks (GCN), graph attention networks (GAT), hyperbolic neural networks (HNN), and hyperbolic graph convolutions (HGCN). By utilizing the protein sequence information, all of these models can predict the interaction between proteins. Fourteen PPI datasets are extracted and utilized to compare the prediction performance of all these methods. The experimental results show that hyperbolic graph neural networks tend to have a better performance than the other methods on the protein-related datasets.

Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions

Background

Development of new methods for analysis of protein–protein interactions (PPIs) at molecular and nanometer scales gives insights into intracellular signaling pathways and will improve understanding of protein functions, as well as other nanoscale structures of biological and abiological origins. Recent advances in computational tools, particularly the ones involving modern deep learning algorithms, have been shown to complement experimental approaches for describing and rationalizing PPIs. However, most of the existing works on PPI predictions use protein-sequence information, and thus have difficulties in accounting for the three-dimensional organization of the protein chains.

Results

In this study, we address this problem and describe a PPI analysis based on a graph attention network, named Struct2Graph, for identifying PPIs directly from the structural data of folded protein globules. Our method is capable of predicting the PPI with an accuracy of 98.89% on the balanced set consisting of an equal number of positive and negative pairs. On the unbalanced set with the ratio of 1:10 between positive and negative pairs, Struct2Graph achieves a fivefold cross validation average accuracy of 99.42%. Moreover, Struct2Graph can potentially identify residues that likely contribute to the formation of the protein–protein complex. The identification of important residues is tested for two different interaction types: (a) Proteins with multiple ligands competing for the same binding area, (b) Dynamic protein–protein adhesion interaction. Struct2Graph identifies interacting residues with 30% sensitivity, 89% specificity, and 87% accuracy.

Conclusions

In this manuscript, we address the problem of prediction of PPIs using a first of its kind, 3D-structure-based graph attention network (code available at https://github.com/baranwa2/Struct2Graph). Furthermore, the novel mutual attention mechanism provides insights into likely interaction sites through its unsupervised knowledge selection process. This study demonstrates that a relatively low-dimensional feature embedding learned from graph structures of individual proteins outperforms other modern machine learning classifiers based on global protein features. In addition, through the analysis of single amino acid variations, the attention mechanism shows preference for disease-causing residue variations over benign polymorphisms, demonstrating that it is not limited to interface residues.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04910-9.

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

At the heart of the cellular machinery through the regulation of cellular functions, protein–protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.

Accurate prediction of virus-host protein-protein interactions via a Siamese neural network using deep protein sequence embeddings

Prediction and understanding of virus-host protein-protein interactions (PPIs) have relevance for the development of novel therapeutic interventions. In addition, virus-like particles open novel opportunities to deliver therapeutics to targeted cell types and tissues. Given our incomplete knowledge of PPIs on the one hand and the cost and time associated with experimental procedures on the other, we here propose a deep learning approach to predict virus-host PPIs. Our method (Siamese Tailored deep sequence Embedding of Proteins [STEP]) is based on recent deep protein sequence embedding techniques, which we integrate into a Siamese neural network. After showing the state-of-the-art performance of STEP on external datasets, we apply it to two use cases, severe acute respiratory syndrome coronavirus 2 and John Cunningham polyomavirus, to predict virus-host PPIs. Altogether our work highlights the potential of deep sequence embedding techniques originating from the field of NLP as well as explainable artificial intelligence methods for the analysis of biological sequences.

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Deep learning approach (STEP) predicts virus protein to human host protein interactions

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It is based on recent deep protein sequence embeddings and Siamese neural network

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Prediction of PPIs of the JCV VP1 protein and of the SARS-CoV-2 spike protein

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Identify parts of sequences that most likely contribute to the PPI using explainable AI

The development of novel cell and tissue-specific therapies requires a profound knowledge about protein-protein interactions (PPIs). Identifying these PPIs with experimental approaches such as biochemical assays or yeast two-hybrid screens is cumbersome, costly, and at the same time difficult to scale. Computational approaches can help to prioritize huge amounts of possible PPIs by learning from biological sequences plus already known PPIs. In this work, we developed an approach that is based on recent deep protein sequence embedding techniques, which we integrate into a Siamese neural network architecture. We use this approach to train models by using protein sequence information and known PPIs. We apply the models to two use cases to predict virus protein to human host interactions. Altogether our work highlights the potential of deep sequence embedding techniques as well as explainable artificial intelligence methods for the analysis of biological sequence data.

A Survey on Deep Networks Approaches in Prediction of Sequence-Based Protein–Protein Interactions

The prominence of protein–protein interactions (PPIs) in system biology with diverse biological procedures has become the topic to discuss because it acts as a fundamental part in predicting the protein function of the target protein and drug ability of molecules. Numerous researches have been published to predict PPIs computationally because they provide an alternative solution to laboratory trials and a cost-effective way of predicting the most likely set of interactions at the entire proteome scale. In recent computational methods, deep learning has become a buzzword with numerous scientific researches. This paper presents, for the first time, a comprehensive survey of sequence-based PPI prediction by three popular deep learning architectures i.e. deep neural networks, convolutional neural networks and recurrent neural networks and its variants. The thorough survey discussed herein carefully mined every possible information, can help the researchers to further explore the success in this area.

The significance of the fusion partner gene genomic neighborhood analysis in translocation-defined tumors

INTRODUCTION

This study presents a novel molecular parameter potentially co-defining tumor biology-the total tumor suppressor gene (TSG) count at chromosomal loci harboring genes rearranged in fusion-defined tumors. It belongs to the family of molecular parameters created using a black-box approach.

METHOD

It is based on a public curated Texas TSG database. Its data are regrouped based on individual genes loci using another public database (Genecards). The total TSG count for NTRK (NTRK1; OMIM: 191315; NTRK2; OMIM: 600456; NTRK3; OMIM: 191316), NRG1 (OMIM: 142445), and RET (OMIM: 164761) rearranged tumors in patients treated with a theranostic approach is calculated using the results of recently published studies.

RESULTS

Altogether 138 loci containing at least three TSGs are identified. These include 21 "extremely hot" spots, with 10 to 28 TSGs mapping to a given locus. However, the study falls short of finding a correlation between tumor regression or patient survival and the TSG count owing to a low number of cases meeting the study criteria.

CONCLUSION

The total TSG count alone cannot predict the biology of translocation-defined tumors. The addition of other parameters, including microsatellite instability (MSI), tumor mutation burden (TMB), homologous recombination repair deficiency (HRD), and copy number heterogeneity (CNH), might be helpful. Thus a multi-modal data integration is advocated. We believe that large scale studies should evaluate the significance and value of the total TSG count.

Computational Network Inference for Bacterial Interactomics

Since the large-scale experimental characterization of protein–protein interactions (PPIs) is not possible for all species, several computational PPI prediction methods have been developed that harness existing data from other species. While PPI network prediction has been extensively used in eukaryotes, microbial network inference has lagged behind. However, bacterial interactomes can be built using the same principles and techniques; in fact, several methods are better suited to bacterial genomes. These predicted networks allow systems-level analyses in species that lack experimental interaction data. This review describes the current network inference and analysis techniques and summarizes the use of computationally-predicted microbial interactomes to date.

Network Pharmacology- and Molecular Docking-Based Identification of Potential Phytocompounds from Argyreia capitiformis in the Treatment of Inflammation

The methanolic extract of Argyreia capitiformis stem was examined for anti-inflammatory activities following network pharmacology analysis and molecular docking study. Based on gas chromatography-mass spectrometry (GC-MS) analysis, 49 compounds were identified from the methanolic extract of A. capitiformis stem. A network pharmacology analysis was conducted against the identified compounds, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology analysis of biological processes and molecular functions were performed. Six proteins (IL1R1, IRAK4, MYD88, TIRAP, TLR4, and TRAF6) were identified from the KEGG pathway analysis and subjected to molecular docking study. Additionally, six best ligand efficiency compounds and positive control (aspirin) from each protein were evaluated for their stability using the molecular dynamics simulation study. Our study suggested that IL1R1, IRAK4, MYD88, TIRAP, TLR4, and TRAF6 proteins may be targeted by compounds in the methanolic extract of A. capitiformis stem to provide anti-inflammatory effects.

Protein-protein interactions: Methods, databases, and applications in virus-host study

Almost all the cellular processes in a living system are controlled by proteins: They regulate gene expression, catalyze chemical reactions, transport small molecules across membranes, and transmit signal across membranes. Even, a viral infection is often initiated through virus-host protein interactions. Protein-protein interactions (PPIs) are the physical contacts between two or more proteins and they represent complex biological functions. Nowadays, PPIs have been used to construct PPI networks to study complex pathways for revealing the functions of unknown proteins. Scientists have used PPIs to find the molecular basis of certain diseases and also some potential drug targets. In this review, we will discuss how PPI networks are essential to understand the molecular basis of virus-host relationships and several databases which are dedicated to virus-host interaction studies. Here, we present a short but comprehensive review on PPIs, including the experimental and computational methods of finding PPIs, the databases dedicated to virus-host PPIs, and the associated various applications in protein interaction networks of some lethal viruses with their hosts.

Computational predictions for protein sequences of COVID-19 virus via machine learning algorithms

The rapid spread of coronavirus disease (COVID-19) has become a worldwide pandemic and affected more than 15 million patients reported in 27 countries. Therefore, the computational biology carrying this virus that correlates with the human population urgently needs to be understood. In this paper, the classification of the human protein sequences of COVID-19, according to the country, is presented based on machine learning algorithms. The proposed model is based on distinguishing 9238 sequences using three stages, including data preprocessing, data labeling, and classification. In the first stage, data preprocessing's function converts the amino acids of COVID-19 protein sequences into eight groups of numbers based on the amino acids' volume and dipole. It is based on the conjoint triad (CT) method. In the second stage, there are two methods for labeling data from 27 countries from 0 to 26. The first method is based on selecting one number for each country according to the code numbers of countries, while the second method is based on binary elements for each country. According to their countries, machine learning algorithms are used to discover different COVID-19 protein sequences in the last stage. The obtained results demonstrate 100% accuracy, 100% sensitivity, and 90% specificity via the country-based binary labeling method with a linear support vector machine (SVM) classifier. Furthermore, with significant infection data, the USA is more prone to correct classification compared to other countries with fewer data. The unbalanced data for COVID-19 protein sequences is considered a major issue, especially as the US's available data represents 76% of a total of 9238 sequences. The proposed model will act as a prediction tool for the COVID-19 protein sequences in different countries.

Improved prediction of protein-protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines

In this paper, for accurate prediction of protein-protein interaction (PPI), a novel hybrid classifier is developed by combining the functional-link Siamese neural network (FSNN) with the light gradient boosting machine (LGBM) classifier. The hybrid classifier (FSNN-LGBM) uses the fusion of features derived using pseudo amino acid composition and conjoint triad descriptors. The FSNN extracts the high-level abstraction features from the raw features and LGBM performs the PPI prediction task using these abstraction features. On performing 5-fold cross-validation experiments, the proposed hybrid classifier provides average accuracies of 98.70 and 98.38%, respectively, on the intraspecies PPI data sets of Saccharomyces cerevisiae and Helicobacter pylori. Similarly, the average accuracies for the interspecies PPI data sets of the Human-Bacillus and Human-Yersinia data sets are 98.52 and 97.40%, respectively. Compared with the existing methods, the hybrid classifier achieves higher prediction accuracy on the independent test sets and network data sets. The improved prediction performance obtained by the FSNN-LGBM makes it a flexible and effective PPI prediction model.

Drug Repurposing in Oncology: Current Evidence and Future Direction

BACKGROUND

Drug repurposing, the application of known drugs and compounds with a primary non-oncology purpose, might be an attractive strategy to offer more effective treatment options to cancer patients at a low cost and reduced time.

METHODS

This review described a total of 10 kinds of non-oncological drugs from more than 100 mechanical studies as well as evidence from population-based studies. The future direction of repurposed drug screening is discussed by using patient-derived tumor organoids.

RESULTS

Many old drugs showed previously unknown effects or off-target effects and can be intelligently applied for cancer chemoprevention and therapy. The identification of repurposed drugs needs to combine evidence from mechanical studies and population-based studies. Due to the heterogeneity of cancer, patient-derived tumor organoids can be used to screen the non-oncological drugs in vitro.

CONCLUSION

These identified old drugs could be repurposed in oncology and might be added as adjuvants and finally benefit patients with cancers.

Protein analysis and stability: Overcoming trial-and-error by grouping according to physicochemical properties

Today proteins are possibly the most important class of substances. Yet new tasks for proteins are still often solved by trial-and-error approaches. However, in some areas these euphemistically called "screening approaches" are not suitable. E.g. stability tests just take too long and therefore require a more strategic, target-orientated concept. This concept is available by grouping proteins according to their physicochemical properties and then pulling out the right drawer for new tasks. These properties include size, then charge and hydrophobicity as well as their patchinesses, and the degree of order. In addition, solubility, the content of (free) enthalpy, aromatic-amino-acid- and α/β-frequency as well as helix capping, and corresponding patchiness, the number of specific motifs and domains as well as the typical concentration range can be helpful to discriminate between different groups of proteins. Analyzing correlations will reduce the necessary amount of parameters and additional ones, which may be still undiscovered at the present time, can be identified looking at protein subgroups with similar physicochemical properties which still behave heterogeneously. Step-by-step the methodology will be improved. Possibly protein stability will be the driver of this process, but all other areas such as production, purification and analytics including sample pre-treatment and the choice of appropriate separation conditions for e.g. chromatography and electrophoresis will profit from a rational strategy.

Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization

Accurate assessment of protein-protein interactions (PPIs) is critical to deciphering disease mechanisms and developing novel drugs, and with rapidly growing PPI data, the need for more efficient predictive methods is emerging. We propose here a symmetric logistic matrix factorization (symLMF)-based approach to predict PPIs, especially useful for large PPI networks. Benchmarked against two widely used datasets (Saccharomyces cerevisiae and Homo sapiens benchmarks) and their extended versions, the symLMF-based method proves to outperform most of the state-of-the-art data-driven methods applied to human PPIs, and it shows a performance comparable to those of deep learning methods despite its conceptual and technical simplicity and efficiency. Tests performed on humans, yeast, and tissue (brain and liver)- and disease (neurodegenerative and metabolic disorders)-specific datasets further demonstrate the high capability to capture the hidden interactions. Notably, many "de novo predictions" made by symLMF are verified to exist in PPI databases other than those used for training/testing the method, indicating that the method could be of broad utility as a simple, yet efficient and accurate, tool applicable to PPI datasets.

2D Zernike polynomial expansion: Finding the protein-protein binding regions

We present a method for efficiently and effectively assessing whether and where two proteins can interact with each other to form a complex. This is still largely an open problem, even for those relatively few cases where the 3D structure of both proteins is known. In fact, even if much of the information about the interaction is encoded in the chemical and geometric features of the structures, the set of possible contact patches and of their relative orientations are too large to be computationally affordable in a reasonable time, thus preventing the compilation of reliable interactome. Our method is able to rapidly and quantitatively measure the geometrical shape complementarity between interacting proteins, comparing their molecular iso-electron density surfaces expanding the surface patches in term of 2D Zernike polynomials. We first test the method against the real binding region of a large dataset of known protein complexes, reaching a success rate of 0.72. We then apply the method for the blind recognition of binding sites, identifying the real region of interaction in about 60% of the analyzed cases. Finally, we investigate how the efficiency in finding the right binding region depends on the surface roughness as a function of the expansion order.

Ab-initio binding of barnase–barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach

Receptor–ligand interactions are involved in various biological processes, therefore understanding the binding mechanism and ability to predict the binding mode are essential for many biological investigations. While many computational methods exist to predict the 3D structure of the corresponding complex provided the knowledge of the monomers, here we use the newly developed DelPhiForce steered Molecular Dynamics (DFMD) approach to model the binding of barstar to barnase to demonstrate that first-principles methods are also capable of modeling the binding. Essential component of DFMD approach is enhancing the role of long-range electrostatic interactions to provide guiding force of the monomers toward their correct binding orientation and position. Thus, it is demonstrated that the DFMD can successfully dock barstar to barnase even if the initial positions and orientations of both are completely different from the correct ones. Thus, the electrostatics provides orientational guidance along with pulling force to deliver the ligand in close proximity to the receptor.

Multifaceted protein-protein interaction prediction based on Siamese residual RCNN

Motivation

Sequence-based protein–protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information.

Results

We present an end-to-end framework, PIPR (Protein–Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short.

Availability and implementation

The implementation is available at https://github.com/muhaochen/seq_ppi.git.

Supplementary information

Supplementary data are available at Bioinformatics online.

EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks

Discovering important proteins in Protein-Protein Interaction (PPI) networks has attracted a lot of attention in recent years. Most of the previous work applies different network centrality measures such as Closeness, Betweenness, PageRank and many others to discover the most influential proteins in PPI networks. Although entropy is a well-known graph-based method in computer science, according to our knowledge, it is not used in the biology domain for this purpose. In this paper, first, we annotate the human PPI network with available annotation data. Second, we introduce a new concept called annotation-context that describes each protein according to annotation data of its neighbors. Third, we apply an entropy measure to discover proteins with varied annotation-context. Empirical results indicate that our proposed method succeeded in (1) differentiating essential and non-essential proteins in PPI networks with annotation data; (2) outperforming centrality measures in the task of discovering essential nodes; (3) predicting new annotated proteins based on existing annotation data.

Intrinsically disordered protein domains in flavivirus infection

Intrinsically disordered protein regions are at the core of biological processes and involved in key protein-ligand interactions. The Flavivirus proteins, of viruses of great biomedical importance such as Zika and dengue viruses, exemplify this. Several proteins of these viruses have disordered regions that are of the utmost importance for biological activity. Disordered proteins can adopt several conformations, each able to interact with and/or bind to different ligands. In fact, such interactions can help stabilize a particular fold. Moreover, by being promiscuous in the number of target molecules they can bind to, these protein regions increase the number of functions that their small proteome (10 proteins) can achieve. A folding energy waterfall better describes the protein folding landscape of these proteins. A disordered protein can be thought as rolling down the folding energy cascade, in order "to fall, fold and function". This is the case of many viral protein regions, as seen in the flaviviruses proteome. Given their small size, flaviviruses are a good model system for understanding the role of intrinsically disordered protein regions in viral function. Finally, studying these viruses disordered protein regions will certainly contribute to the development of therapeutic approaches against such promising (yet challenging) targets.

Construction and Comprehensive Analysis of a Molecular Association Network via lncRNA-miRNA -Disease-Drug-Protein Graph

One key issue in the post-genomic era is how to systematically describe the associations between small molecule transcripts or translations inside cells. With the rapid development of high-throughput “omics” technologies, the achieved ability to detect and characterize molecules with other molecule targets opens the possibility of investigating the relationships between different molecules from a global perspective. In this article, a molecular association network (MAN) is constructed and comprehensively analyzed by integrating the associations among miRNA, lncRNA, protein, drug, and disease, in which any kind of potential associations can be predicted. More specifically, each node in MAN can be represented as a vector by combining two kinds of information including the attribute of the node itself (e.g., sequences of ncRNAs and proteins, semantics of diseases and molecular fingerprints of drugs) and the behavior of the node in the complex network (associations with other nodes). A random forest classifier is trained to classify and predict new interactions or associations between biomolecules. In the experiment, the proposed method achieved a superb performance with an area under curve (AUC) of 0.9735 under a five-fold cross-validation, which showed that the proposed method could provide new insight for exploration of the molecular mechanisms of disease and valuable clues for disease treatment.

Dark Proteome Database: Studies on Dark Proteins

The dark proteome, as we define it, is the part of the proteome where 3D structure has not been observed either by homology modeling or by experimental characterization in the protein universe. From the 550.116 proteins available in Swiss-Prot (as of July 2016), 43.2% of the eukarya universe and 49.2% of the virus universe are part of the dark proteome. In bacteria and archaea, the percentage of the dark proteome presence is significantly less, at 12.6% and 13.3% respectively. In this work, we present a necessary step to complete the dark proteome picture by introducing the map of the dark proteome in the human and in other model organisms of special importance to mankind. The most significant result is that around 40% to 50% of the proteome of these organisms are still in the dark, where the higher percentages belong to higher eukaryotes (mouse and human organisms). Due to the amount of darkness present in the human organism being more than 50%, deeper studies were made, including the identification of ‘dark’ genes that are responsible for the production of so-called dark proteins, as well as the identification of the ‘dark’ tissues where dark proteins are over represented, namely, the heart, cervical mucosa, and natural killer cells. This is a step forward in the direction of gaining a deeper knowledge of the human dark proteome.

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.

WITHDRAWN: Structural and functional characterization for interaction of silver nanoparticles with ergostrol in Trichoderma harzianum

This article has been withdrawn: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been withdrawn at the request of the editor and publisher. The publisher regrets that an error occurred which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error.