期刊
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
卷 29, 期 1, 页码 93-101出版社
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2010.05.005
关键词
Protein structure alignment; Ligand superposition; Flexible ligand analysis; Bipartite matching; Dynamic programming; Clique enumeration
类别
资金
- Bill and Melinda Gates Foundation
- Natural Sciences and Engineering Research Council of Canada
Ligand-based active site alignment is a widely adopted technique for the structural analysis of protein-ligand complexes. However, existing tools for ligand alignment treat the ligands as rigid objects even though most biological ligands are flexible. We present LigAlign, an automated system for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment. Crown Copyright (C) 2010 Published by Elsevier Inc. All rights reserved.
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