ArticleNucleic acids research2018
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.Nucleic acids research · 2025Article
- Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure.Interdisciplinary sciences, computational life sciences · 2024Review
- Parental experiences orchestrate locust egg hatching synchrony by regulating nuclear export of precursor miRNA.Nature communications · 2024Article
- Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics · 2023Article
- The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.Nucleic acids research · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Arf GTPase activates the WAVE regulatory complex through a distinct binding site.Science advances · 2022Article
- Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- The chemistry of snake venom and its medicinal potential.Nature reviews. Chemistry · 2022Review
- Recombinant nanobody against MUC1 tandem repeats inhibits growth, invasion, metastasis, and vascularization of spontaneous mouse mammary tumors.Molecular oncology · 2022Article
- From complete cross-docking to partners identification and binding sites predictions.PLoS computational biology · 2022Article
- Distinct RPA domains promote recruitment and the helicase-nuclease activities of Dna2.Nature communications · 2021Article
- InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.Nucleic acids research · 2021Article
- Integrin α11β1 is a receptor for collagen XIII.Cell and tissue research · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Article
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- LightDock goes information-driven.Bioinformatics (Oxford, England) · 2020Article
- Coarse-grained (hybrid) integrative modeling of biomolecular interactions.Computational and structural biotechnology journal · 2020Review
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction. For this purpose, we added modules in InterEvDock2 for automatic template search and comparative modeling of the input proteins. The InterEvDock2 pipeline was benchmarked on 812 complexes for which unbound homology models of the two partners and co-evolutionary information are available in the PPI4DOCK database. InterEvDock2 identified a correct model among the top 10 consensus in 29% of these cases (compared to 15-24% for individual scoring functions) and at least one correct interface residue among 10 predicted in 91% of these cases. InterEvDock2 is thus a unique protein docking server, designed to be useful for the experimental biology community. The InterEvDock2 web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/.
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