Journal
COMPUTATIONAL BIOLOGY AND CHEMISTRY
Volume 74, Issue -, Pages 39-48Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.compbiolchem.2018.02.012
Keywords
GNU parallel; AutoDock; Open babel; Virtual screening; Parallel processing; Ligand preparation
Funding
- Department of Bio-Technology (DBT), Ministry of Science and Technology, Government of India through DBT-JRF Fellowship [DBT/2015/VRF/363]
- DBT Rapid Grant for Young Investigator (RGYI) scheme [BT/PR6476/GBD/27/496/2013]
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High throughput virtual screening plays a crucial role in hit identification during the drug discovery process. With the rapid increase in the chemical libraries, virtual screening process becomes computationally challenging, thereby posing a demand for efficiently parallelized software pipelines. Here we present a GNU Parallel based pipeline-POAP that is programmed to run Open Babel and AutoDock suite under highly optimized parallelization. The ligand preparation module is a unique feature in POAP, as it offers extensive options for geometry optimization, conformer generation, parallelization and also quarantines erroneous datasets for seamless operation. POAP also features multi receptor docking that can be utilized for comparative virtual screening and drug repurposing studies. As demonstrated using different structural datasets, POAP proves to be an efficient pipeline that enables high scalability, seamless operability, dynamic file handling and optimal utilization of CPU's for computationally demanding tasks. POAP is distributed freely under GNU GPL license and can be downloaded at https://github.com/inpacdb/POAP. (C) 2018 Elsevier Ltd. All rights reserved.
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