Simulation methods for protein structure fluctuations

✍ Scribed by Scott H. Northrup; J. Andrew McCammon

• Publisher: Wiley (John Wiley & Sons)
• Year: 1980
• Tongue: English
• Weight: 875 KB
• Volume: 19
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1980.360190506

✦ Synopsis

Abstract

Three numerical techniques for generating thermally accessible configurations of globular proteins are considered; these techniques are the molecular dynamics method, the Metropolis Monte Carlo method, and a modified Monte Carlo method which takes account of the forces acting on the protein atoms. The molecular dynamics method is shown to be more efficient than either of the Monte Carlo methods. Because it may be necessary to use Monte Carlo methods in certain important types of sampling problems, the behavior of these methods is examined in some detail. It is found that an acceptance ratio close to 1/6 yields optimum efficiency for the Metropolis method, in contrast to what is often assumed. This result, together with the overall inefficiency of the Monte Carlo methods, appears to arise from the anisotropic forces acting on the protein atoms due to their covalent bonding. Possible ways of improving the Monte Carlo methods are suggested.