SAMPL4 & DOCK3.7: lessons for automated docking procedures.
SAMPL4 & DOCK3.7: lessons for automated docking procedures.
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Sampl4＆Dock3.7：自动对接程序的课程。
DOI：
10.1007/s10822-014-9722-6
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发表时间：
2014-03
影响因子：
3.5
通讯作者：
Weiss, Dahlia R.
中科院分区：
文献类型：
--
作者：
Coleman, Ryan G.;Sterling, Teague;Weiss, Dahlia R.
SAMPL4挑战用于测试当前自动化方法，用于分子对接管道DOCK 3.7的溶剂化能、虚拟筛选、姿态和亲和力预测。此外，结合亲和力的一阶模型被提出作为任何预测结合亲和力的方法的里程碑。在挑战过程中，关于分子对接软件的几个重要发现：1）配体的溶剂化能比SAMPL4中使用的任何其他方法差五倍，包括类似快速的方法，2）HIV整合酶是具有挑战性的靶标，但在虚拟筛选和姿态预测方面，3）分子对接网格大小可能非常重要，在默认设置下发现了严重的错误，这些默认设置已经针对所有未来工作进行了调整。总的来说，从SAMPL4的经验教训表明，许多变化的分子对接工具，而不仅仅是DOCK 3.7，可以提高国家的艺术。未来的困难和项目将进行讨论。
The SAMPL4 challenges were used to test current automated methods for solvation energy, virtual screening, pose and affinity prediction of the molecular docking pipeline DOCK 3.7. Additionally, first-order models of binding affinity were proposed as milestones for any method predicting binding affinity. Several important discoveries about the molecular docking software were made during the challenge: 1) Solvation energies of ligands were five-fold worse than any other method used in SAMPL4, including methods that were similarly fast, 2) HIV Integrase is a challenging target, but automated docking on the correct allosteric site performed well in terms of virtual screening and pose prediction (compared to other methods) but affinity prediction, as expected, was very poor, 3) Molecular docking grid sizes can be very important, serious errors were discovered with default settings that have been adjusted for all future work. Overall, lessons from SAMPL4 suggest many changes to molecular docking tools, not just DOCK 3.7, that could improve the state of the art. Future difficulties and projects will be discussed.
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