bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.
bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.
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bSiteFinder，一种基于结构比对的改进的蛋白质结合位点预测服务器：更准确、更省时
DOI：
10.1186/s13321-016-0149-z
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发表时间：
2016
影响因子：
8.6
通讯作者：
Zhu R
中科院分区：
文献类型：
--
作者：
Gao J;Zhang Q;Liu M;Zhu L;Wu D;Cao Z;Zhu R
蛋白质结合位点预测为蛋白质功能注释和基于结构的药物设计奠定了基础。随着蛋白质结构数量的增加，基于结构比对的算法成为蛋白质结合位点预测的主流方法。然而，现有的算法没有充分利用日益增多的三维蛋白质-配体复合物结构（结合蛋白），在比对、模板选择和模板聚类等方面还有待改进。在此，我们建立了迄今为止最大的结合模板数据库，并进行了严格的质量控制。并在此基础上开发了bSiteMap作为蛋白质结合位点预测服务器。通过在算法中引入同源索引、链长索引、复杂模板稳定性和优化多模板聚类，服务器的效率得到了显著提高。此外，对于结合数据集或未结合数据集的测试，准确度比其他算法高约2- 10%。对于210个绑定数据集，bSiteMap实现了高达94.8%的高准确率（MCC 0.95）。对于另外48个结合/未结合的数据集，bSiteMap实现了高达93.8%的结合蛋白（MCC 0.95）和85.4%的未结合蛋白（MCC 0.72）的高准确度。我们的bSitefinder服务器可以在http：//binfo.shmtu.edu.cn/bsitefinder/上免费获得，源代码在方法页面上提供。 bSitefinder（http：//binfo.shmtu.edu.cn/bsitefinder/）是基于目前最大的结合模板数据库开发的蛋白质结合位点预测服务器，经过严格的质量控制。通过在算法中引入同源索引、链长索引、复杂模板稳定性和优化多模板聚类，服务器的效率得到了显著提高。更重要的是，对于绑定数据集或未绑定数据集的测试，准确率比其他算法高出约2- 10%。http://binfo.shmtu.edu.cn/bsitefinder/我们的工作为蛋白质的功能注释和基于结构的药物设计奠定了基础。随着三维蛋白质-配体复合物结构数量的不断增加，我们的服务器应该更准确，更耗时。
Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein–ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2–10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset. For 210 bound dataset, bSiteFinder achieved high accuracies up to 94.8 % (MCC 0.95). For another 48 bound/unbound dataset, bSiteFinder achieved high accuracies up to 93.8 % for bound proteins (MCC 0.95) and 85.4 % for unbound proteins (MCC 0.72). Our bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/, and the source code is provided at the methods page. bSiteFinder (http://binfo.shmtu.edu.cn/bsitefinder/) as a protein-binding sites prediction server was developed based on the largest database of bound templates so far with stringent quality control. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server have been significantly improved. What’s more, the accuracy was approximately 2–10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset An online bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/. Our work lays a foundation for functional annotation of protein and structure-based drug design. With ever increasing numbers of three-dimensional protein–ligand complex structures, our server should be more accurate and less time-consuming.