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Journal of Computer-Aided Molecular Design

, Volume 22, Issue 9, pp 681–691 | Cite as

A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers

  • Roman J. Dorfman
  • Karl M. Smith
  • Brian B. Masek
  • Robert D. Clark
Article

Abstract

This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. Sampling can be tailored to a specific structural domain (e.g., peptides) by extracting torsional profiles from specific datasets and subsequently applying them to target molecules outside the reference set. The programs that handle creation of the knowledge-based torsional profiles and conformer generation per se are separate and so can be used independently or sequentially, depending on the task at hand. The conformational ensembles produced are contrasted with those generated using local minimization approaches. They are also quantitatively compared with a broader range of techniques in terms of speed and the ability to reproduce bound ligand conformations found in complexes with proteins.

Keywords

Conformer generation Conformational sampling Bioactive conformation Shape-searching Docking Pharmacophores 

Notes

Acknowledgments

Many thanks to Dr. Edmond Abrahamian (Tripos) for infusing common sense into this publication, noting errors, suggesting additional areas to cover, and asking searching questions.

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Roman J. Dorfman
    • 1
  • Karl M. Smith
    • 1
  • Brian B. Masek
    • 1
  • Robert D. Clark
    • 1
  1. 1.Tripos Informatics Research CenterSt. LouisUSA

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