title: GPURFSCREEN: a GPU based virtual screening tool using random forest classifier.
abstract: BACKGROUND
  In-silico methods are an integral part of modern drug discovery paradigm. Virtual screening, an in-silico method, is used to refine data models and reduce the chemical space on which wet lab experiments need to be performed. Virtual screening of a ligand data model requires large scale computations, making it a highly time consuming task. This process can be speeded up by implementing parallelized algorithms on a Graphical Processing Unit (GPU).
  
  
  RESULTS
  Random Forest is a robust classification algorithm that can be employed in the virtual screening. A ligand based virtual screening tool (GPURFSCREEN) that uses random forests on GPU systems has been proposed and evaluated in this paper. This tool produces optimized results at a lower execution time for large bioassay data sets. The quality of results produced by our tool on GPU is same as that on a regular serial environment.
  
  
  CONCLUSIONS
  Considering the magnitude of data to be screened, the parallelized virtual screening has a significantly lower running time at high throughput. The proposed parallel tool outperforms its serial counterpart by successfully screening billions of molecules in training and prediction phases.
authors.affiliation: Department of Computer Science and Engineering, National Institute of Technology Calicut, NITC Campus, Calicut, Kerala 673601 India.
authors.forename: P B
authors.initials: PB
authors.lastname: Jayaraj
authors.affiliation: Department of Computer Science and Engineering, National Institute of Technology Calicut, NITC Campus, Calicut, Kerala 673601 India.
authors.forename: Mathias K
authors.initials: MK
authors.lastname: Ajay
authors.affiliation: Department of Computer Science and Engineering, National Institute of Technology Calicut, NITC Campus, Calicut, Kerala 673601 India.
authors.forename: M
authors.initials: M
authors.lastname: Nufail
authors.affiliation: Department of Computer Science and Engineering, National Institute of Technology Calicut, NITC Campus, Calicut, Kerala 673601 India.
authors.forename: G
authors.initials: G
authors.lastname: Gopakumar
authors.affiliation: Center for Cheminformatics, Open Source Pharma, No. 22, World Trade Centre, Malleswaram, Bengaluru, Karnataka 560055 India.
authors.forename: U C A
authors.initials: UC
authors.lastname: Jaleel
keywords: CUDA; GPU computing; In-silico drug discovery; Ligand based drug discovery; Random forest classifier; Virtual screening