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Description
  • The AutoDock suite is widely used molecular docking software consisting of two main programs -- AutoGrid for precomputation of potential grid maps and AutoDock for docking into potential grid maps. In this paper, the acceleration of potential maps generation based on AutoGrid and its implementation called FastGrid is presented. The most computationally expensive algorithms are accelerated using GPU, the rest of algorithms run on CPU with asymptotically lower time complexity that has been obtained using more sophisticated data structures than in the original AutoGrid code. Moreover, the CPU implementation is parallelized to fully exploit computational power of machines that are equipped with more CPU cores than GPUs. Our implementation outperforms original AutoGrid more than 400x for large, but quite common molecules and sufficiently large grids.
  • The AutoDock suite is widely used molecular docking software consisting of two main programs -- AutoGrid for precomputation of potential grid maps and AutoDock for docking into potential grid maps. In this paper, the acceleration of potential maps generation based on AutoGrid and its implementation called FastGrid is presented. The most computationally expensive algorithms are accelerated using GPU, the rest of algorithms run on CPU with asymptotically lower time complexity that has been obtained using more sophisticated data structures than in the original AutoGrid code. Moreover, the CPU implementation is parallelized to fully exploit computational power of machines that are equipped with more CPU cores than GPUs. Our implementation outperforms original AutoGrid more than 400x for large, but quite common molecules and sufficiently large grids. (en)
Title
  • FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking
  • FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking (en)
skos:prefLabel
  • FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking
  • FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking (en)
skos:notation
  • RIV/00216224:14330/10:00045786!RIV11-MSM-14330___
http://linked.open...avai/riv/aktivita
http://linked.open...avai/riv/aktivity
  • S, Z(MSM0021622413), Z(MSM0021622419)
http://linked.open...iv/cisloPeriodika
  • 6+
http://linked.open...vai/riv/dodaniDat
http://linked.open...aciTvurceVysledku
http://linked.open.../riv/druhVysledku
http://linked.open...iv/duvernostUdaju
http://linked.open...titaPredkladatele
http://linked.open...dnocenehoVysledku
  • 258841
http://linked.open...ai/riv/idVysledku
  • RIV/00216224:14330/10:00045786
http://linked.open...riv/jazykVysledku
http://linked.open.../riv/klicovaSlova
  • acceleration; GPU; CUDA; AutoDock; AutoGrid (en)
http://linked.open.../riv/klicoveSlovo
http://linked.open...odStatuVydavatele
  • SK - Slovenská republika
http://linked.open...ontrolniKodProRIV
  • [CC796A4E5184]
http://linked.open...i/riv/nazevZdroje
  • Computing and Informatics
http://linked.open...in/vavai/riv/obor
http://linked.open...ichTvurcuVysledku
http://linked.open...cetTvurcuVysledku
http://linked.open...UplatneniVysledku
http://linked.open...v/svazekPeriodika
  • 29
http://linked.open...iv/tvurceVysledku
  • Filipovič, Jiří
  • Prokop, Martin
  • Olšák, Marek
http://linked.open...n/vavai/riv/zamer
issn
  • 1335-9150
number of pages
http://localhost/t...ganizacniJednotka
  • 14330
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