istar: a web platform for large-scale protein-ligand docking.
istar: a web platform for large-scale protein-ligand docking.
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DOI：
10.1371/journal.pone.0085678
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Wong MH
中科院分区：
文献类型：
--
作者：
Li H;Leung KS;Ballester PJ;Wong MH
蛋白质-配体对接是药物发现过程起点设计的关键计算方法。我们希望使用我们流行的对接引擎 idock 实现大规模对接自动化，因此开发了一个名为 istar 的可公开访问的网络平台。无需繁琐的软件安装，用户就可以使用我们的网站提交工作。我们的istar网站支持1）按所需的分子特性过滤配体并预览要对接的配体数量，2）实时监控工作进度，3）可视化配体构象并输出idock预测的自由能和配体效率，RF-Score预测的结合亲和力，推定的氢键和供应商信息以方便购买，这三个有用的功能通常是其他在线对接平台（如DOCK Blaster或iScreen）所缺乏的。我们从 ZINC 数据库的 All Clean 子集中收集了 17,224,424 个配体，并将我们的对接引擎 idock 改进为 2.0 版本，进一步提高对接速度和准确性，并集成 RF-Score 作为替代重评分功能。为了将 idock 2.0 与最先进的 AutoDock Vina 1.1.2 进行比较，我们分别对 PDBbind v2012 精炼集和 CSAR NRC HiQ Set 24Sept2010 的 2,897 个和 343 个蛋白质-配体复合物进行了重新评分基准和重新对接基准，并对 12 种不同蛋白质和 3,000 个不同配体进行了执行时间基准。分子量。结果显示，在各种场景下，idock 的成功率相当，但对接速度至少优于 AutoDock Vina 8.69 倍，最多 37.51 倍。当在 PDBbind v2012 核心集上进行评估时，我们的 istar 平台与 RF-Score 相结合，成功地重现了对接构象的实验结合亲和力和预测结合亲和力之间分别高达 0.855 和 0.859 的 Pearson 相关系数和 Spearman 相关系数。 istar 可在 http://istar.cse.cuhk.edu.hk/idock 免费获取。
Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar is freely available at http://istar.cse.cuhk.edu.hk/idock.
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