title: Hydrophilic aromatic residue and in silico structure for carbohydrate binding module.
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/.
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.
authors.forename: Wei-Yao
authors.initials: WY
authors.lastname: Chou
authors.forename: Tun-Wen
authors.initials: TW
authors.lastname: Pai
authors.forename: Ting-Ying
authors.initials: TY
authors.lastname: Jiang
authors.forename: Wei-I
authors.initials: WI
authors.lastname: Chou
authors.forename: Chuan-Yi
authors.initials: CY
authors.lastname: Tang
authors.forename: Margaret Dah-Tsyr
authors.initials: MD
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D002241:Carbohydrates / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D000596:Amino Acids; D002241:Carbohydrates; D008024:Ligands; D011506:Proteins