Title: | Structural alphabet motif discovery and a structural motif database |
Authors: | Ku, Shih-Yen Hu, Yuh-Jyh 分子醫學與生物工程研究所 資訊工程學系 Institute of Molecular Medicine and Bioengineering Department of Computer Science |
Keywords: | Protein structures;Structural alphabets;Structural motifs;Sequence motifs;Motif-finding tools |
Issue Date: | 1-Jan-2012 |
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/. (C) 2011 Elsevier Ltd. All rights reserved. |
URI: | http://dx.doi.org/10.1016/j.compbiomed.2011.10.013 http://hdl.handle.net/11536/15284 |
ISSN: | 0010-4825 |
DOI: | 10.1016/j.compbiomed.2011.10.013 |
Journal: | COMPUTERS IN BIOLOGY AND MEDICINE |
Volume: | 42 |
Issue: | 1 |
Begin Page: | 93 |
End Page: | 105 |
Appears in Collections: | Articles |
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