An approach to detection of protein structural motifs using an encoding scheme of backbone conformations.
This paper presents an approach to detection of protein structural motifs. In our approach, first all protein backbone conformations are converted into character strings using an encoding scheme. Then we use the Smith-Waterman local alignment algorithm to detect common structural motifs. By comparing results with the PROSITE regular expression patterns, our method can detect several motifs which the PROSITE patterns fail to detect.
Matsuda
H
H
Department of Informatics and Mathematical Science, Graduate School of Engineering Science, Osaka University, Japan. matsuda@ics.es.osaka-u.ac.jp
Taniguchi
F
F
Hashimoto
A
A
D000595:Amino Acid Sequence; D002135:Calcium-Binding Proteins / Q000737:chemistry; D003198:Computer Simulation; D003459:Crystallins / Q000737:chemistry; D019992:Databases as Topic; D016208:Databases, Factual; D019143:Evolution, Molecular; D016247:Information Storage and Retrieval; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software
D002135:Calcium-Binding Proteins; D003459:Crystallins; D011506:Proteins