Journal of Computer-Aided Molecular Design

, Volume 8, Issue 6, pp 695–708 | Cite as

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

  • Thomas Huber
  • Andrew E. Torda
  • Wilfred F. van Gunsteren
Research Papers

Summary

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.

Key words

Conformational search Computer simulation Molecular dynamics Cyclosporin A 

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Copyright information

© ESCOM Science Publishers B.V 1994

Authors and Affiliations

  • Thomas Huber
    • 1
  • Andrew E. Torda
    • 1
  • Wilfred F. van Gunsteren
    • 1
  1. 1.Physical ChemistryETH ZentrumZürichSwitzerland

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