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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F09%3A00037320%21RIV10-MSM-14310___
rdf:type
skos:Concept n13:Vysledek
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 the original AutoGrid more than $400\times$ 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 the original AutoGrid more than $400\times$ 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/00216224:14310/09:00037320!RIV10-MSM-14310___
n3:aktivita
n18:S n18:Z
n3:aktivity
S, Z(MSM0021622413), Z(MSM0021622419)
n3:dodaniDat
n19:2010
n3:domaciTvurceVysledku
n10:4842138 n10:3993779 n10:5428599
n3:druhVysledku
n12:D
n3:duvernostUdaju
n21:S
n3:entitaPredkladatele
n4:predkladatel
n3:idSjednocenehoVysledku
314713
n3:idVysledku
RIV/00216224:14310/09:00037320
n3:jazykVysledku
n14:eng
n3:klicovaSlova
molecular docking; autogrid; autodock; acceleration; GPU; high performance computing
n3:klicoveSlovo
n7:GPU n7:high%20performance%20computing n7:autodock n7:autogrid n7:molecular%20docking n7:acceleration
n3:kontrolniKodProRIV
[C459DF3A666C]
n3:mistoKonaniAkce
Znojmo, Czech Republic
n3:mistoVydani
Brno, Czech Republic
n3:nazevZdroje
MEMICS 2009: Fifth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science
n3:obor
n5:IN
n3:pocetDomacichTvurcuVysledku
3
n3:pocetTvurcuVysledku
3
n3:rokUplatneniVysledku
n19:2009
n3:tvurceVysledku
Filipovič, Jiří Prokop, Martin Olšák, Marek
n3:typAkce
n16:WRD
n3:zahajeniAkce
2009-01-01+01:00
n3:zamer
n6:MSM0021622413 n6:MSM0021622419
s:numberOfPages
8
n17:hasPublisher
Masarykova univerzita; Vysoké učení technické v Brně
n20:isbn
978-80-87342-04-6
n9:organizacniJednotka
14310