VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization.
VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization.
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DOI：
10.3390/ijms22115807
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发表时间：
2021-05-28
影响因子：
5.6
通讯作者：
Arthanari H
中科院分区：
文献类型：
--
作者：
Gorgulla C;Çınaroğlu SS;Fischer PD;Fackeldey K;Wagner G;Arthanari H
基于蚁群优化(ACO)算法的对接程序Plants具有许多先进的分子对接特性。其中包括多重评分函数、显式可置换水分子建模的可能性，以及包含实验约束。在这里，我们在VirtualFlow(VirtualFlow Ants)中增加了对植物的支持，这为初步的虚拟筛选和重新评分过程增加了一种有价值的方法。此外，我们增加了对MOL2格式的配位体库的支持，以及将PDBQT格式的配位体库即时转换为MOL2格式，以赋予VirtualFlow ANT关于配位体库的更大灵活性。利用Open Babel和程序孢子进行即时转换。我们将VirtualFlow Ants应用于Google Cloud上涉及Keap1的测试系统，最高可达128,000个CPU，观察到的扩展行为近似为线性。此外，我们还调整了植物的几个中心对接参数(如速度参数或蚂蚁数量)，并为产生的10个对接场景中的每一个筛选了1000万个化合物。我们分析了他们的对接分数和平均对接次数，这是虚拟放映的关键因素。通过VirtualFlow蚂蚁对植物进行超大型虚拟筛选的可能性为计算机药物发现开辟了新的途径。
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.
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