CIMO-ESA, Instituto Politécnico de Bragança, Campus de Sta Apolónia, Apartado 1172, 5301-855 Bragança, Portugal.
J Cheminform. 2010 Oct 28;2(1):10. doi: 10.1186/1758-2946-2-10.
Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters.
MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections.
MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.
使用分子对接对小分子进行虚拟筛选已成为药物发现的重要工具。然而，大规模的虚拟筛选耗时且通常需要专用的计算机集群。有许多软件工具可使用 AutoDock4 进行虚拟筛选，但它们需要访问专用的 Linux 计算机集群。也没有用于使用 Vina 在计算机集群上进行虚拟筛选的软件。在本文中，我们提出了 MOLA，这是一种易于使用的图形用户界面工具，可在可引导的非专用计算机集群中自动执行使用 AutoDock4 和/或 Vina 的并行虚拟筛选。
MOLA 自动执行多项任务，包括：配体准备、并行 AutoDock4/Vina 作业分配和结果分析。当虚拟筛选项目完成后，将打开一个 OpenOffice 电子表格文件，其中列出了根据结合能和与活性位点的距离对配体进行排序的结果。所有结果文件都可以自动记录在 USB 闪存驱动器或使用 VirtualBox 的硬盘驱动器上。MOLA 在我们开发的定制 Live CD GNU/Linux 操作系统内部运行，该操作系统绕过了集群中使用的计算机上安装的原始操作系统。该操作系统从主节点上的 CD 引导，然后通过以太网连接将其他计算机作为从节点集群。
MOLA 是一种理想的虚拟筛选工具，适用于经验有限的用户，并且只有数量有限的多平台异构计算机，并且无法访问专用的 Linux 计算机集群。当虚拟筛选项目完成后，只需重新启动计算机即可回到其原始操作系统。MOLA 的新颖之处在于，任何可用的与平台无关的计算机都可以添加到集群中，而无需使用计算机硬盘驱动器，也不会干扰已安装的操作系统。使用 10 个处理器的集群，并且潜在的最大加速为 10 倍，MOLA 的并行算法使用 AutoDock4 实现了 8.64 倍的加速，使用 Vina 实现了 8.60 倍的加速。
