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

BMC Bioinformatics

Research

Maxim Totrov¹ 

[1] Molsoft LLC, 3366 N Torrey Pines Ct, 92037, La Jolla, CA, USA;

关键词: Protein Data Bank;    Atomic Property;    Pharmacophoric Feature;    Chymosin;    Adenosyl;   

DOI  :  10.1186/1471-2105-12-S1-S35

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Totrov; licensee BioMed Central Ltd. 2011