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Normal-Mode-Analysis–Monitored Energy Minimization Procedure for Generating Small–Molecule Bound Conformations

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  • Qi Wang
  • Yuan-Ping Pang

Abstract

The energy minimization of a small molecule alone does not automatically stop at a local minimum of the potential energy surface of the molecule if the minimum is shallow, thus leading to folding of the molecule and consequently hampering the generation of the bound conformation of a guest in the absence of its host. This questions the practicality of virtual screening methods that use conformations at local minima of their potential energy surfaces (local minimum conformations) as potential bound conformations. Here we report a normal-mode-analysis–monitored energy minimization (NEM) procedure that generates local minimum conformations as potential bound conformations. Of 22 selected guest–host complex crystal structures with guest structures possessing up to four rotatable bonds, all complexes were reproduced, with guest mass–weighted root mean square deviations of

Suggested Citation

  • Qi Wang & Yuan-Ping Pang, 2007. "Normal-Mode-Analysis–Monitored Energy Minimization Procedure for Generating Small–Molecule Bound Conformations," PLOS ONE, Public Library of Science, vol. 2(10), pages 1-7, October.
    • Handle: RePEc:plo:pone00:0001025
    DOI: 10.1371/journal.pone.0001025
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    1. Qi Wang & Yuan-Ping Pang, 2007. "Preference of Small Molecules for Local Minimum Conformations when Binding to Proteins," PLOS ONE, Public Library of Science, vol. 2(9), pages 1-10, September.
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