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首页> 外文期刊>Computer Methods and Programs in Biomedicine: An International Journal Devoted to the Development, Implementation and Exchange of Computing Methodology and Software Systems in Biomedical Research and Medical Practice >Design of a grid service-based platform for in silico protein-ligand screenings.
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Design of a grid service-based platform for in silico protein-ligand screenings.

机译：基于网格服务的计算机硅蛋白配体筛选平台的设计。

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Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP towrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound "drug-like" subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.
机译：网格计算提供了强大的替代方案，可以在全球范围内跨不同机构共享资源，从而无需集中式超级计算机即可运行计算密集型的科学应用程序。在软件开发方面已经投入了大量精力，该软件可以在基于网格的基础架构上部署遗留应用程序，并有效地利用可用资源。从网格资源的使用中可以极大受益的一个领域是药物发现，因为分子对接模拟是发现过程不可或缺的一部分。在本文中，我们提供了一个可扩展的可重用平台，用于使用分子对接仿真软件DOCK在计算网格上编排大型虚拟筛选实验。软件组件被应用于多个级别，以创建自动化的工作流程，包括输入数据传递，作业计划，状态查询以及输出的收集，以可管理的方式显示以进行进一步分析。这是通过使用Opal OP将DOCK应用程序包装为网格服务，以及将PERL用于数据处理而实现的，从而减轻了对网格基础设施广泛知识的需求。有了适当的平台，就可以在PRAGMA网格测试平台上使用DOCK 5.4的MPI版本成功地针对酶的催化位点筛选ZINC 2,066,906化合物“药物样”子集数据库。筛选需要11.56天的实验室时间，并在7个群集中使用了200个处理器。

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