ArticleNucleic acids research2021
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.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
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- Gut-primed neutrophils activate Kupffer cells to promote hepatic injury in mouse sepsis.Nature communications · 2025Article
- FcRn-dependent IgG accumulation in adipose tissue unmasks obesity pathophysiology.Cell metabolism · 2025Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- Neutrophils disrupt B-1a cell homeostasis by targeting Siglec-G to exacerbate sepsis.Cellular & molecular immunology · 2024Article
- Mitigation of TDP-43 toxic phenotype by an RGNEF fragment in amyotrophic lateral sclerosis models.Brain : a journal of neurology · 2024Article
- ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Senktide blocks aberrant RTN3 interactome to retard memory decline and tau pathology in social isolated Alzheimer's disease mice.Protein & cell · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- GRAMM Web Server for Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins.International journal of molecular sciences · 2023Article
- Latent generative landscapes as maps of functional diversity in protein sequence space.Nature communications · 2023Article
- Modeling Protein Complexes and Molecular Assemblies Using Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A comparative analysis of fruit fly and human glutamate dehydrogenases inFrontiers in cell and developmental biology · 2023Article
- HDOCK update for modeling protein-RNA/DNA complex structures.Protein science : a publication of the Protein Society · 2022Article
- Mitofusin2 PromotesStem cells international · 2022Article
- The Zip4 protein directly couples meiotic crossover formation to synaptonemal complex assembly.Genes & development · 2022Article
- Proteo3Dnet: a web server for the integration of structural information with interactomics data.Nucleic acids research · 2021Article
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10 authors.
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Abstract
The InterEvDock3 protein docking server exploits the constraints of evolution by multiple means to generate structural models of protein assemblies. The server takes as input either several sequences or 3D structures of proteins known to interact. It returns a set of 10 consensus candidate complexes, together with interface predictions to guide further experimental validation interactively. Three key novelties were implemented in InterEvDock3 to help obtain more reliable models: users can (i) generate template-based structural models of assemblies using close and remote homologs of known 3D structure, detected through an automated search protocol, (ii) select the assembly models most consistent with contact maps from external methods that implement covariation-based contact prediction with or without deep learning and (iii) exploit a novel coevolution-based scoring scheme at atomic level, which leads to significantly higher free docking success rates. The performance of the server was validated on two large free docking benchmark databases, containing respectively 230 unbound targets (Weng dataset) and 812 models of unbound targets (PPI4DOCK dataset). Its effectiveness has also been proven on a number of challenging examples. The InterEvDock3 web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock3/.
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