title: LigAlign: flexible ligand-based active site alignment and analysis.
abstract: 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.
authors: Department of Computer Science, Univ. of Toronto, Toronto, Ontario, Canada.
authors: Abraham
authors: A
authors: Heifets
authors: Ryan H
authors: RH
authors: Lilien
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008969:Molecular Sequence Data; D009243:NAD / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D008024:Ligands; D009243:NAD; D006418:Heme