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BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S35. doi: 10.1186/1471-2105-12-S1-S35.

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites.

Author information

  • Molsoft LLC,3366 N Torrey Pines Ct, La Jolla, CA 92037, USA. max@molsoft.com

Abstract

A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly homologous and convergent binding sites. Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB.

PMID:
21342566
[PubMed - indexed for MEDLINE]
PMCID:
PMC3044291
Free PMC Article

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