Bullock Casey W, Jacob Reed B, McDougal Owen M, Hampikian Greg, Andersen Tim
Computer Science Department, Boise State University, Boise, Idaho 83725, USA.
BMC Res Notes. 2010 Nov 8;3:289. doi: 10.1186/1756-0500-3-289.
The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.
DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations.
DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.
由于计算集群和云的可访问性，将计算建模应用于合理设计药物和表征大分子受体已被证明越来越有用。AutoDock是一个用于模拟配体与受体结合相互作用的著名且强大的软件程序。在其当前版本中，AutoDock需要大量用户时间来设置和运行作业以及收集结果。本文介绍了DockoMatic，这是一个用户友好的图形用户界面（GUI）应用程序，它简化并自动化了用于高通量筛选配体与受体相互作用的AutoDock作业的创建和管理。
DockoMatic允许用户在单台计算机或集群上调用和管理AutoDock作业，包括评估二级配体相互作用的作业。它还自动化了收集、汇总和查看结果的过程。此外，DockoMatic可根据单字母氨基酸缩写字符串自动创建肽配体的.pdb文件。
DockoMatic通过促进配体和AutoDock作业的创建和管理，显著降低了管理多个AutoDock作业的复杂性。
