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J Med Chem. 2005 May 5;48(9):3313-8.

Conformation mining: an algorithm for finding biologically relevant conformations.

Author information

  • 1Rational Discovery LLC, 555 Bryant Street #467, Palo Alto, California 94301, USA. sputta@rationaldiscovery.com

Abstract

Discovering essential features shared by active compounds, an important step in drug-design, is complicated by conformational flexibility. We present a new algorithm to efficiently mine the conformational space of multiple actives and find small subsets of conformations likely to be biologically relevant. The approach identifies chemical and steric similarities between actives, providing insight into features important for binding when structural data are absent. Validation studies (thrombin and CDK2 data) produce alignments similar to protein-based alignments.

PMID:
15857136
DOI:
10.1021/jm049066l
[PubMed - indexed for MEDLINE]
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