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

Christina E.M. Schindler, Isaure Chauvot de Beauchêne, Sjoerd J. de Vries, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

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. Proteins 2017; 85:391–398.

Original languageEnglish
Pages (from-to)391-398
Number of pages8
JournalProteins: Structure, Function and Bioinformatics
Volume85
Issue number3
DOIs
StatePublished - 1 Mar 2017
Externally publishedYes

Keywords

  • docking minimization
  • elastic network model
  • induced fit
  • protein-protein complex formation
  • protein-protein interaction

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