Structural alphabet motif discovery and a structural motif database

Authors:
Shih-Yen Ku;Yuh-Jyh Hu
Affiliations:
Department of Computer Science, National Chiao Tung University, 1001 Tashuei Rd., Hsinchu, Taiwan;Department of Computer Science, National Chiao Tung University, 1001 Tashuei Rd., Hsinchu, Taiwan and Institute of Biomedical Engineering, National Chiao Tung University, 1001 Tashuei Rd., Hsinchu ...
Venue:
Computers in Biology and Medicine
Year:
2012

Citing 2
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Combinatorial Approaches to Finding Subtle Signals in DNA Sequences

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
SMotif: a server for structural motifs in proteins

Bioinformatics

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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/.