Local elevation: a method for improving the searching properties of molecular dynamics simulation

J Comput Aided Mol Des. 1994 Dec;8(6):695-708. doi: 10.1007/BF00124016.

Abstract

The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Simulation
  • Computer-Aided Design*
  • Cyclosporine / chemistry
  • Drug Design*
  • Models, Chemical
  • Molecular Conformation
  • Pentanes / chemistry
  • Software Design
  • Thermodynamics*

Substances

  • Pentanes
  • pentane
  • Cyclosporine