The Virtual Laboratory: a toolset to enable distributed molecular modelling for drug design on the World-Wide Grid
The Virtual Laboratory: a toolset to enable distributed molecular modelling for drug design on the World-Wide Grid
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DOI：
10.1002/cpe.704
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发表时间：
2003-01-01
影响因子：
2
通讯作者：
Abramson, D
中科院分区：
文献类型：
--
作者：
Buyya, R;Branson, K;Abramson, D
计算网格正在成为共享和聚合地理分布资源的新范例，用于解决科学、工程和商业中的大规模计算和数据密集型问题。然而。这些环境中的应用程序开发、资源管理和调度是一项复杂的任务。在本文中，我们通过利用现有网格技术来说明虚拟实验室环境的开发，以实现对地理分布资源上的药物设计进行分子建模。它涉及针对蛋白质靶标筛选化学数据库 (CDB) 中的数百万种化合物，以识别那些可能用于药物设计的化合物。我们使用 Nimrod-G 参数规范语言将现有的分子对接应用程序转换为参数扫描应用程序，以便在分布式系统上执行。我们开发了新工具，可以从远程资源访问 CDB 中的配体记录/分子。 Nimrod-G 资源代理与分子 CDB 数据代理一起用于全球网格 (WWG) 资源上的对接作业的调度和按需处理。结果证明了 Nimrod-G 和网格计算虚拟实验室工具的易用性和强大功能。版权所有 (C) 2003 John Wiley Sons, Ltd.
Computational Grids are emerging as a new paradigm for sharing and aggregation of geographically distributed resources for solving large-scale compute and data intensive problems in science, engineering and commerce. However. application development, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the development of a Virtual Laboratory environment by leveraging existing Grid technologies to enable molecular modelling for drug design on geographically distributed resources. It involves screening millions of compounds in the chemical database (CDB) against a protein target to identify those with potential use for drug design. We have used the Nimrod-G parameter specification language to transform the existing molecular docking application into a parameter sweep application for executing on distributed systems. We have developed new tools for enabling access to ligand records/molecules in the CDB from remote resources. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of docking jobs on the World-Wide Grid (WWG) resources. The results demonstrate the ease of use and power of the Nimrod-G and virtual laboratory tools for grid computing. Copyright (C) 2003 John Wiley Sons, Ltd.