ArticleNucleic acids research2016
InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions.Briefings in bioinformatics · 2025Article
- Structure-Based Deep Learning Framework for Modeling Human-Gut Bacterial Protein Interactions.Proteomes · 2025Article
- A comprehensive survey of scoring functions for protein docking models.BMC bioinformatics · 2025Article
- Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning.Biomolecules · 2025Review
- Amyloid transformations of phenol soluble modulin α1 in Staphylococcus aureus and their modulation deploying a prenylated chalcone.Scientific reports · 2024Article
- Parental experiences orchestrate locust egg hatching synchrony by regulating nuclear export of precursor miRNA.Nature communications · 2024Article
- Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits.Computational and structural biotechnology journal · 2023Article
- Protein-protein interaction prediction methods: from docking-based to AI-based approaches.Biophysical reviews · 2022Review
- DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling.Frontiers in molecular biosciences · 2021Article
- Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape ofFrontiers in molecular biosciences · 2021Review
- Chasing coevolutionary signals in intrinsically disordered proteins complexes.Scientific reports · 2020Article
- Performance of ZDOCK and IRAD in CAPRI rounds 39-45.Proteins · 2020Article
- The HDOCK server for integrated protein-protein docking.Nature protocols · 2020Article
- Characterization of the inhibition mechanism of a tissuefactor inhibiting single-chain variable fragment: a combined computational approach.Journal of molecular modeling · 2020Article
- Identifying protein-protein interface via a novel multi-scale local sequence and structural representation.BMC bioinformatics · 2019Article
- Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- What method to use for protein-protein docking?Current opinion in structural biology · 2019Review
- More efficient screening of protein-protein complex model structures for reducing the number of candidates.Biophysics and physicobiology · 2019Article
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6 authors.
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Abstract
The structural modeling of protein-protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/.
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