Detecting Native Protein Folds among Large Decoy Sets with the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model
- Richard A. Friesner
Published Online: 13 MAR 2002
DOI: 10.1002/0471224421.ch8
Copyright © 2002 John Wiley & Sons, Inc.
Book Title
Computational Methods for Protein Folding, Volume 120
Additional Information
How to Cite
Wallqvist, A., Gallicchio, E., Felts, A. K. and Levy, R. M. (2002) Detecting Native Protein Folds among Large Decoy Sets with the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model, in Computational Methods for Protein Folding, Volume 120 (ed R. A. Friesner), John Wiley & Sons, Inc., New York, USA. doi: 10.1002/0471224421.ch8
Editor Information
Columbia University, New York, New York, USA
Publication History
- Published Online: 13 MAR 2002
- Published Print: 4 JAN 2002
Book Series:
Book Series Editors:
- I. Prigogine3,4,
- Stuart A. Rice5
Series Editor Information
- 3
Center for Studies in Statistical Mechanics and Complex Systems, The University of Texas, Austin, Texas, USA
- 4
International Solvay Institutes, Université Libre de Bruxelles, Brussels, Belgium
- 5
Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois, USA
ISBN Information
Print ISBN: 9780471209553
Online ISBN: 9780471224426
- Summary
- Chapter
Keywords:
- native protein folds;
- decoy sets;
- OPLS all-atom potential;
- Born solvent model
Summary
In this work the authors show that the all atom (OPLS-AA) force field for proteins together with a surface integral formulation of the generalized Born model (SGB) is capable of discriminating between native and non-native folds among large sets of compact decoy structures. Validation of the scoring protocol is performed on a large database of well-packed misfolded and near-native protein conformations generated by an algorithm designed to cover exhaustively the relevant parts of conformational space. Two additional decoy data sets of misfolded proteins and of predicted protein structures from the Critical Assessment of Techniques for Protein Structure Prediction (CASP) are also used to illustrate the method and its utility. It is also shown that some aspects of the SGB model results can be mimicked by a screened electrostatic energy, although the SGB approximation provides a better discriminatory measure between non-native and native states.