InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs

By Chloé Quignot, Julien Rey, Jinchao Yu, Pierre Tufféry, Raphaël Guérois, Jessica Andreani. 2018

50 citations recorded by the source corpus.

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/.

Subfields: Computational Theory and Mathematics, Molecular Biology

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In Computational Theory and Mathematics

1. Dima Kozakov
2. Israel T. Desta
3. Kathryn A. Porter
4. Sandor Vajda
5. Junmei Wang
6. John C. Dearden

In Molecular Biology

1. Dima Kozakov
2. Kathryn A. Porter
3. Sandor Vajda
4. Gaoqi Weng
5. Israel T. Desta
6. Tingjun Hou
7. Feng Zhu
8. Zhe Wang

Citations in the corpus

• HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, background): “A number of template-free docking servers have been developed and released to the public, such as ATTRACT (5), ClusPro (6), HADDOCK (7), ZDOCK server (8), SwarmDock (9), pyDockSAXS (10), pyDockWeb (11), InterEvDock2 (12), GRAMM-X (13), RosettaDock server (14), PatchDock (15), Hex server (16), 3D-Gar”
• What Method to Use for Protein-Protein Docking? (2019, methodology): “We also suggest that, depending on template quality, switching between template-based and free methods is likely to be useful for predicting the structures of heterooligomers, as it has already been implemented in some docking servers [6,7].”