Accelerating molecular docking calculations using graphics processing units

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KORB, Oliver, Thomas STÜTZLE, Thomas EXNER, 2011. Accelerating molecular docking calculations using graphics processing units. In: Journal of Chemical Information and Modeling. 51(4), pp. 865-876. ISSN 1549-9596. eISSN 1549-960X

@article{Korb2011-04-25Accel-18364, title={Accelerating molecular docking calculations using graphics processing units}, year={2011}, doi={10.1021/ci100459b}, number={4}, volume={51}, issn={1549-9596}, journal={Journal of Chemical Information and Modeling}, pages={865--876}, author={Korb, Oliver and Stützle, Thomas and Exner, Thomas} }

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/18364"> <dc:contributor>Korb, Oliver</dc:contributor> <dcterms:bibliographicCitation>Publ. in: Journal of chemical information and modeling ; 51 (2011), 4. - pp. 865-876</dcterms:bibliographicCitation> <dc:contributor>Stützle, Thomas</dc:contributor> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-02-09T11:14:03Z</dcterms:available> <dc:contributor>Exner, Thomas</dc:contributor> <dcterms:issued>2011-04-25</dcterms:issued> <dcterms:title>Accelerating molecular docking calculations using graphics processing units</dcterms:title> <dc:creator>Exner, Thomas</dc:creator> <dc:language>eng</dc:language> <dcterms:abstract xml:lang="eng">The generation of molecular conformations and the evaluation of interaction potentials are common tasks in molecular modeling applications, particularly in protein−ligand or protein−protein docking programs. In this work, we present a GPU-accelerated approach capable of speeding up these tasks considerably. For the evaluation of interaction potentials in the context of rigid protein−protein docking, the GPU-accelerated approach reached speedup factors of up to over 50 compared to an optimized CPU-based implementation. Treating the ligand and donor groups in the protein binding site as flexible, speedup factors of up to 16 can be observed in the evaluation of protein−ligand interaction potentials. Additionally, we introduce a parallel version of our protein−ligand docking algorithm PLANTS that can take advantage of this GPU-accelerated scoring function evaluation. We compared the GPU-accelerated parallel version to the same algorithm running on the CPU and also to the highly optimized sequential CPU-based version. In terms of dependence of the ligand size and the number of rotatable bonds, speedup factors of up to 10 and 7, respectively, can be observed. Finally, a fitness landscape analysis in the context of rigid protein−protein docking was performed. Using a systematic grid-based search methodology, the GPU-accelerated version outperformed the CPU-based version with speedup factors of up to 60.</dcterms:abstract> <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/18364"/> <dc:creator>Stützle, Thomas</dc:creator> <dc:creator>Korb, Oliver</dc:creator> <dcterms:rights rdf:resource="http://nbn-resolving.org/urn:nbn:de:bsz:352-20140905103605204-4002607-1"/> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-02-09T11:14:03Z</dc:date> <dc:rights>deposit-license</dc:rights> </rdf:Description> </rdf:RDF>

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