Zhang Shuxing, Kumar Kamal, Jiang Xiaohui, Wallqvist Anders, Reifman Jaques
Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
BMC Bioinformatics. 2008 Feb 27;9:126. doi: 10.1186/1471-2105-9-126.
Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial.
We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried.
DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.
基于分子对接的虚拟筛选是药物研发中的一项重要工具，用于显著减少待研究的可能化合物数量。除了选择具有适当评分函数的合理对接策略外，另一个技术挑战是在合理时间内对数百万种化合物进行计算机模拟筛选。为应对这一挑战，有必要使用高性能计算（HPC）平台和技术。然而，开发一个能有效利用其组件的集成HPC系统并非易事。
我们开发了一个名为DOVIS的应用程序，它使用AutoDock（版本3）作为对接引擎，并在Linux集群上并行运行。DOVIS能够高效地将大量（数百万）小分子（配体）与受体对接，每个处理器每天可筛选500至1000种化合物。此外，在DOVIS中，对接过程完全集成且自动化，即通过图形用户界面指定输入，计算与Linux集群排队系统完全集成以进行并行处理，结果可以可视化并查询。
DOVIS消除了与大规模高通量虚拟筛选相关的大部分复杂性和组织问题，并为AutoDock用户在Linux集群平台上使用该软件提供了方便高效的解决方案。
