title: Structural alphabet motif discovery and a structural motif database.
abstract: This study proposes a general framework for structural motif discovery. The framework is based on a modular design in which the system components can be modified or replaced independently to increase its applicability to various studies. It is a two-stage approach that first converts protein 3D structures into structural alphabet sequences, and then applies a sequence motif-finding tool to these sequences to detect conserved motifs. We named the structural motif database we built the SA-Motifbase, which provides the structural information conserved at different hierarchical levels in SCOP. For each motif, SA-Motifbase presents its 3D view; alphabet letter preference; alphabet letter frequency distribution; and the significance. SA-Motifbase is available at http://bioinfo.cis.nctu.edu.tw/samotifbase/.
authors.affiliation: Department of Computer Science, National Chiao Tung University, 1001 Tashuei Rd., Hsinchu, Taiwan.
authors.forename: Shih-Yen
authors.initials: SY
authors.lastname: Ku
authors.forename: Yuh-Jyh
authors.initials: YJ
authors.lastname: Hu
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030562:Databases, Protein; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins