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Statements

Subject Item
n2:RIV%2F00216224%3A14330%2F10%3A00045786%21RIV11-MSM-14330___
rdf:type
n13:Vysledek skos:Concept
dcterms: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.
dcterms:title
FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking
skos:prefLabel
FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking FastGrid -- The Accelerated AutoGrid Potential Maps Generation for Molecular Docking
skos:notation
RIV/00216224:14330/10:00045786!RIV11-MSM-14330___
n4:aktivita
n6:Z n6:S
n4:aktivity
S, Z(MSM0021622413), Z(MSM0021622419)
n4:cisloPeriodika
6+
n4:dodaniDat
n10:2011
n4:domaciTvurceVysledku
n8:5428599 n8:4842138 n8:3993779
n4:druhVysledku
n11:J
n4:duvernostUdaju
n18:S
n4:entitaPredkladatele
n15:predkladatel
n4:idSjednocenehoVysledku
258841
n4:idVysledku
RIV/00216224:14330/10:00045786
n4:jazykVysledku
n14:eng
n4:klicovaSlova
acceleration; GPU; CUDA; AutoDock; AutoGrid
n4:klicoveSlovo
n7:AutoDock n7:AutoGrid n7:acceleration n7:CUDA n7:GPU
n4:kodStatuVydavatele
SK - Slovenská republika
n4:kontrolniKodProRIV
[CC796A4E5184]
n4:nazevZdroje
Computing and Informatics
n4:obor
n17:IN
n4:pocetDomacichTvurcuVysledku
3
n4:pocetTvurcuVysledku
3
n4:rokUplatneniVysledku
n10:2010
n4:svazekPeriodika
29
n4:tvurceVysledku
Olšák, Marek Prokop, Martin Filipovič, Jiří
n4:zamer
n5:MSM0021622413 n5:MSM0021622419
s:issn
1335-9150
s:numberOfPages
11
n16:organizacniJednotka
14330