Computational techniques for efficient conformational sampling of proteins

Curr Opin Struct Biol. 2008 Apr;18(2):134-9. doi: 10.1016/j.sbi.2007.12.001. Epub 2008 Jan 22.

Abstract

In this review, we summarize the computational methods for sampling the conformational space of biomacromolecules. We discuss the methods applicable to find only lowest energy conformations (global minimization of the potential-energy function) and to generate canonical ensembles (canonical Monte Carlo method and canonical molecular dynamics method and their extensions). Special attention is devoted to the use of coarse-grained models that enable simulations to be enhanced by several orders of magnitude.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Computer Simulation*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism
  • Thermodynamics

Substances

  • Proteins