A comparison of the Low Mode and Monte Carlo conformational search methods

J Mol Graph Model. 2002 Oct;21(2):129-50. doi: 10.1016/s1093-3263(02)00144-4.

Abstract

The Low Mode (LM) and Monte Carlo (MC) conformational search methods were compared on three diverse molecular systems; (4R, 5S, 6S, 7R)-hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one (1), 2-methoxy-2-phenyl-2-triflouromethyl-N-alpha-methyl benzyl propanamide (2) and a trimeric 39-membered polyazamacrolide (3). We find that either method, or a combination of the methods, is equally efficient at searching the conformational space of the smaller molecular systems while a 50:50 hybrid of Low Mode and Monte Carlo is most efficient at searching the space of the larger molecular system.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amides / chemistry*
  • Fluorobenzenes / chemistry*
  • Heterocyclic Compounds, 1-Ring / chemistry*
  • Hydrogen Bonding
  • Macrolides / chemistry*
  • Models, Molecular
  • Molecular Conformation*
  • Molecular Structure
  • Monte Carlo Method*
  • Software
  • Urea / chemistry

Substances

  • 2-methoxy-2-phenyl-2-trifluoromethyl-N-alpha-methyl benzyl propanamide
  • Amides
  • Fluorobenzenes
  • Heterocyclic Compounds, 1-Ring
  • Macrolides
  • hexahydro-5,6-dihydroxy-1,3,4,7-tetrakis(phenylmethyl)-2H-1,3-diazapin-2-one
  • Urea