kinDOCK: a tool for comparative docking of protein kinase ligands.
kinDOCK: a tool for comparative docking of protein kinase ligands.
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DOI：
10.1093/nar/gkl211
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发表时间：
2006-07-01
影响因子：
14.9
通讯作者：
Labesse G
中科院分区：
文献类型：
--
作者：
Martin L;Catherinot V;Labesse G
KinDOCK是一个新的web服务器，用于分析蛋白激酶的atp结合位点。这种表征是基于已经与其他蛋白激酶共结晶的配体的对接。从蛋白质数据库（PDB）中提取了蛋白质激酶配体复合物的结构库。该文库可以为给定的蛋白激酶提供潜在的配体及其推测的结合方向。蛋白-蛋白结构叠加后，配体从模板复合物转移到靶蛋白激酶。所得到的配合物使用程序SCORE进行评估，以计算理论亲和力。它们可以动态可视化，以便快速映射重要的空间冲突和与特异性和亲和力相关的潜在取代。这些特性允许快速表征蛋白激酶活性位点，包括可能需要适应特定配体的构象变化。此外，还可以在重点文库中识别出有前途的药效团。这些特性将有助于对大型化合物库的虚拟筛选（VS）进行合理化或优化。该服务器及其文档可在。
KinDOCK is a new web server for the analysis of ATP-binding sites of protein kinases. This characterization is based on the docking of ligands already co-crystallized with other protein kinases. A structural library of protein kinase–ligand complexes has been extracted from the Protein Data Bank (PDB). This library can provide both potential ligands and their putative binding orientation for a given protein kinase. After protein–protein structural superposition, the ligands are transferred from the template complexes to the target protein kinase. The resulting complexes are evaluated using the program SCORE to compute a theoretical affinity. They can be dynamically visualized to allow a rapid mapping of important steric clashes and potential substitutions relevant for specificity and affinity. These characteristics allow a quick characterization of protein kinase active sites including conformation changes potentially required to accommodate particular ligands. Additionally, promising pharmacophores can be identified in the focussed library. These features will help to rationalize or optimize virtual screening (VS) on larger chemical compound libraries. The server and its documentation are freely available at .