A gradient-directed Monte Carlo approach for protein design

J Comput Chem. 2010 Aug;31(11):2164-8. doi: 10.1002/jcc.21506.

Abstract

We develop a new global optimization strategy, gradient-directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acids / chemistry
  • Computational Biology / methods*
  • Drug Design*
  • Monte Carlo Method*
  • Protein Conformation
  • Protein Folding
  • Proteins / chemistry*
  • Thermodynamics

Substances

  • Amino Acids
  • Proteins