An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins
An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins
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DOI：
10.1093/protein/gzg065
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发表时间：
2003-07-01
期刊：
影响因子：
--
通讯作者：
Yamane, T
中科院分区：
文献类型：
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作者：
Shionyu-Mitsuyama, C;Shirai, T;Yamane, T
开发了一个计算机程序系统来预测三维（3D）蛋白质结构上的碳水化合物结合位点。该程序通过参考来自碳水化合物-蛋白质复合物的已知3D结构的经验规则来搜索结合位点。从蛋白质数据库中选择了总共80个非冗余的碳水化合物-蛋白质复合物结构用于经验规则构建。在50个已知的复杂结构上测试了预测系统的性能，以确定该系统是否可以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补丁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被检测到在最好的三个预测中，覆盖了目标蛋白中69%的多糖结合位点。
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.