Software
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
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* Corresponding author: Rui MV Abreu ruiabreu@ipb.pt
1 CIMO-ESA, Instituto Politécnico de Bragança, Campus de Sta Apolónia, Apartado 1172, 5301-855 Bragança, Portugal
2 Instituto de Biotecnologia e Bioengenharia, Centro de Genética e Biotecnologia, Universidade de Trás-os-Montes e Alto Douro (CGB-UTAD/IBB), 5001-801, Vila Real, Portugal
3 Centro de Química, Universidade do Minho, Campus de Gualtar 4710-057 Braga, Portugal
Journal of Cheminformatics 2010, 2:10 doi:10.1186/1758-2946-2-10
Published: 28 October 2010Abstract
Background
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.
Implementation
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.
Conclusion
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.