An empirical approach for detecting nucleotide-binding sites on proteins
An empirical approach for detecting nucleotide-binding sites on proteins
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DOI：
10.1093/protein/gzj002
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发表时间：
2006-02-01
影响因子：
2.4
通讯作者：
Shirai, T
中科院分区：
文献类型：
--
作者：
Saito, M;Go, M;Shirai, T
PDB（蛋白质数据库）中的蛋白质结构数据用于构建核苷酸-蛋白质相互作用的经验评分。一个简单的策略来评估周围的碱基部分的核苷酸的蛋白质原子的空间分布进行分类腺嘌呤，鸟嘌呤，烟酰胺和黄素核苷酸结合位点。除了已知的核苷酸结合基序外，经验分数还检测到了具有不同折叠的蛋白质之间共享的其他几个特征。经验得分也被用来预测蛋白质分子上的结合位点，并对预测系统进行了全面的测试。其结果是，腺嘌呤，鸟嘌呤，烟酰胺和黄素网站的检测效率分别为31%，29%，32%和40%。如果具有最佳得分的预测基底位于3.0埃r.m.s.d.内，则预测被判定为成功。已知的配体位置。
Protein structure data in the PDB (Protein Data Bank) were used to construct empirical scores of nucleotide-protein interactions. A simple strategy to evaluate the spatial distribution of protein atoms around the base moieties of nucleotides was applied to categorize adenine, guanine, nicotinamide and flavin nucleotide-binding sites. In addition to the known nucleotide-binding motifs, the empirical scores detected several other features that were shared among proteins with different folds. The empirical scores were also used to predict the binding sites on protein molecules and a comprehensive test of the prediction system was performed. As a result, adenine, guanine, nicotinamide and flavin sites were detected with efficiencies of 31, 29, 32 and 40%, respectively. The predictions were judged to be successful if the predicted base with the best score was located within a 3.0 angstrom r.m.s.d. from the known ligand positions.