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 multiplatform
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.
