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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/28035

Title: Hydrophilic Aromatic Residue and in silico Structure for Carbohydrate Binding Module
Authors: Wei-Yao Chou;Tun-Wen Pai;Ting-Ying Jiang;Wei-I Chou;Chuan-Yi Tang Margaret Dah-Tsyr Chang
Contributors: NTOU:Department of Computer Science and Engineering
國立臺灣海洋大學:資訊工程學系
Keywords: Carbohydrate binding modules(CBM);hydrophilic aromatic residues
Date: 2011-09
Issue Date: 2011-10-21T02:35:21Z
Publisher: PLoS ONE
Abstract: Abstract:Carbohydrate binding modules (CBMs) are found in polysaccharide-targeting enzymes and increase catalytic efficiency. Because only a relatively small number of CBM structures have been solved, computational modeling represents an alternative approach in conjunction with experimental assessment of CBM functionality and ligand-binding properties. An accurate target-template sequence alignment is the crucial step during homology modeling. However, low sequence identities between target/template sequences can be a major bottleneck. We therefore incorporated the predicted hydrophilic aromatic residues (HARs) and secondary structure elements into our feature-incorporated alignment (FIA) algorithm to increase CBM alignment accuracy. An alignment performance comparison for FIA and six others was made, and the greatest average sequence identities and similarities were achieved by FIA. In addition, structure models were built for 817 representative CBMs. Our models possessed the smallest average surface-potential z scores. Besides, a large true positive value for liagnd-binding aromatic residue prediction was obtained by HAR identification. Finally, the pre-simulated CBM structures have been deposited in the Database of Simulated CBM structures (DS-CBMs). The web service is publicly available at http://dscbm.life.nthu.edu.tw/ and http://dscbm.cs.ntou.edu.tw/.
Relation: 6(9), pp.e24814
URI: http://ntour.ntou.edu.tw/handle/987654321/28035
Appears in Collections:[資訊工程學系] 期刊論文

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