Flexible docking and refinement with a coarse-grained protein model using ATTRACT

Sjoerd De Vries, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

40 Scopus citations

Abstract

A coarse-grained (CG) protein model implemented in the ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI Rounds 22-27. For six targets, acceptable or better quality solutions have been submitted corresponding to ∼60% of all targets. For one target, promising results on the prediction of the hydration structure at the protein-protein interface have been achieved. New approaches for the rapid flexible refinement have been developed based on a combination of atomistic representation of the bonded geometry and a CG description of nonbonded interactions. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed. Proteins 2013; 81:2167-2174.

Original languageEnglish
Pages (from-to)2167-2174
Number of pages8
JournalProteins: Structure, Function and Bioinformatics
Volume81
Issue number12
DOIs
StatePublished - Dec 2013
Externally publishedYes

Keywords

  • Docking minimization
  • Elastic network model
  • Induced fit
  • Protein-protein complex formation
  • Protein-protein interaction

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