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Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

Abstract : The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28-36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed.
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https://hal.archives-ouvertes.fr/hal-01505867
Contributor : Isaure Chauvot de Beauchene <>
Submitted on : Tuesday, April 11, 2017 - 7:34:55 PM
Last modification on : Friday, November 24, 2017 - 3:52:01 PM

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Christina Schindler, Isaure Chauvot de Beauchêne, Sjoerd de Vries, Martin Zacharias. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins: Structure, Function, and Genetics, Wiley, 2017, ⟨10.1002/prot.25196⟩. ⟨hal-01505867⟩

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