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 8,64x using AutoDock4 and 8,60x using Vina. 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. When a virtual screening project finishes, the computers can just be restarted to their original operating system. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections.Ĭonclusion: 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. 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. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. 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. Implementation: MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis.
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. Also no software is available for performing virtual screening with Vina using computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters.
However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. Rui MV Abreu1'2*, Hugo JC Froufe1, Maria Joao RP Queiroz3, Isabel CFR Ferreira1īackground: Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
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