Shionyu-Mitsuyama Clara, Shirai Tsuyoshi, Ishida Hirokazu, Yamane Takashi
Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.
Protein Eng. 2003 Jul;16(7):467-78. doi: 10.1093/protein/gzg065.
A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate-protein complexes. A total of 80 non-redundant carbohydrate-protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.
开发了一种计算机程序系统，用于预测三维（3D）蛋白质结构上的碳水化合物结合位点。这些程序通过参考从已知的碳水化合物 - 蛋白质复合物3D结构推导出来的经验规则来搜索结合位点。从蛋白质数据库中总共选择了80个非冗余的碳水化合物 - 蛋白质复合物结构用于构建经验规则。在50个已知的复合物结构上测试了预测系统的性能，以确定该系统是否能够检测到已知的结合位点。当通过预测和已知结合位点的残基片段之间的重叠来评估性能时，在59%的情况下，已知的单糖结合位点在最佳的三个预测中被检测到，这覆盖了目标蛋白质中69%的多糖结合位点。
