Docking Essential Dynamics Eigenstructures

D. Mustard, David William Ritchie

Research output: Contribution to journalArticle

200 Citations (Scopus)

Abstract

This article describes our attempts to dock the targets in CAPRI Rounds 3-5 using Hex 4.2, and it introduces a novel essential dynamics approach to generate multiple feasible conformations for docking. In the blind trial, the basic Hex algorithm found 1 high-accuracy solution for CAPRI Target 12, and several further medium- and low-accuracy solutions for Targets 11, 12, 13, and 14. Subsequent a posteriori docking of the targets using essential dynamics "eigenstructures" was found to give consistently better predictions than rigidly docking only the unbound or model-built starting structures. Some suggestions to improve this promising new approach are presented. (c) 2005 Wiley-Liss, Inc.

Original languageEnglish
Pages (from-to)269-274
Number of pages5
JournalProteins: Structure, Function, and Bioinformatics
Volume60
Issue number2
Early online date24 Jun 2005
DOIs
Publication statusPublished - Aug 2005

Keywords

  • Hex
  • CAPRI
  • protein docking
  • distance constraints
  • essential dynamics
  • eigen-vector analysis
  • eigenstructures
  • polar Fourier correlation
  • structural basis
  • binding
  • complementarity
  • recognition
  • phosphatase
  • subunits
  • domain

Cite this