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 language | English |
|---|---|
| Pages (from-to) | 269-274 |
| Number of pages | 5 |
| Journal | Proteins: Structure, Function, and Bioinformatics |
| Volume | 60 |
| Issue number | 2 |
| Early online date | 24 Jun 2005 |
| DOIs | |
| Publication status | Published - 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