Virtual Screening in the Cloud: How Big Is Big Enough?
Virtual Screening in the Cloud: How Big Is Big Enough?
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DOI：
10.1021/acs.jcim.9b00779
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发表时间：
2020-09-28
影响因子：
5.6
通讯作者：
Sadowski, Jens
中科院分区：
文献类型：
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作者：
Grebner, Christoph;Malmerberg, Erik;Sadowski, Jens
虚拟筛选是计算机辅助药物设计（CADD）的标准工具。在项目早期，通常使用基于配体的相似性搜索方法来寻找合适的命中分子。然而，可以筛选的化合物的数量和所需的时间通常受到计算资源的限制。我们在这里描述了一个高通量的虚拟筛选项目，使用3D相似性（FastROCS）和自动化评估工作流程的猎户座，云计算平台。云资源使这种方法具有完全的可扩展性和灵活性，允许生成和搜索数十亿个虚拟分子，并可以访问以前没有的显式3D虚拟化学空间。我们讨论的搜索空间的大小的影响，寻找新的化学点击和所需的命中列表的大小，以及计算和经济方面的资源扩展。
Virtual screening is a standard tool in Computer-Assisted Drug Design (CADD). Early in a project, it is typical to use ligand-based similarity search methods to find suitable hit molecules. However, the number of compounds which can be screened and the time required are usually limited by computational resources. We describe here a high-throughput virtual screening project using 3D similarity (FastROCS) and automated evaluation workflows on Orion, a cloud computing platform. Cloud resources make this approach fully scalable and flexible, allowing the generation and search of billions of virtual molecules, and give access to an explicit 3D virtual chemistry space not available before. We discuss the impact of the size of the search space with respect to finding novel chemical hits and the size of the required hit list, as well as computational and economical aspects of resource scaling.