AutoDock Vina : Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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Abstract

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

Salvato in:
Autori: Oleg Trott (Scripps Research Institute); Arthur J. Olson iD (Scripps Research Institute)
Pubblicato in: Journal of Computational Chemistry, vol. 31, n. 2, pp. 455-461
Data di pubblicazione:04/06/2009
Editore:Wiley
Tipo di documento:Articolo
Lingua:inglese
DOI: 10.1002/jcc.21334
ISSN:0192-8651, 1096-987X
Accesso aperto: Accesso aperto Bronze: lettura gratuita presso l'editore, senza licenza aperta – Journal of Computational Chemistry
Citazioni ricevute:38.124
Soggetti:
Computational Drug Discovery Methods (Physical Sciences > Computer Science > Computational Theory and Mathematics)
Advanced Chemical Physics Studies (Physical Sciences > Physics and Astronomy > Atomic and Molecular Physics, and Optics)
Protein Structure and Dynamics (Life Sciences > Biochemistry, Genetics and Molecular Biology > Molecular Biology)
AutoDock Vina, molecular docking, virtual screening, scoring functions, binding mode prediction, multithreading, multi-core parallelization, grid map
Identificativi: OpenAlex W2134967712 · PMID 19499576

Dati dell'indice centrale: OpenAlex (licenza CC0).

Riassunto:AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.21334