AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.
Journal
Journal of chemical information and modeling
ISSN: 1549-960X
Titre abrégé: J Chem Inf Model
Pays: United States
ID NLM: 101230060
Informations de publication
Date de publication:
23 08 2021
23 08 2021
Historique:
pubmed:
20
7
2021
medline:
21
10
2021
entrez:
19
7
2021
Statut:
ppublish
Résumé
AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks support for modeling specific features such as macrocycles or explicit water molecules. Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python bindings to facilitate scripting and the development of docking workflows. This work is an effort toward the unification of the features of the AutoDock4 and AutoDock Vina programs. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina.
Identifiants
pubmed: 34278794
doi: 10.1021/acs.jcim.1c00203
pmc: PMC10683950
mid: NIHMS1947068
doi:
Substances chimiques
Ligands
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
3891-3898Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM069832
Pays : United States
Références
J Chem Inf Model. 2020 Dec 28;60(12):6065-6073
pubmed: 33118813
J Chem Theory Comput. 2019 Oct 8;15(10):5161-5168
pubmed: 31505931
J Mol Biol. 1997 Apr 4;267(3):727-48
pubmed: 9126849
J Med Chem. 2012 Jul 26;55(14):6582-94
pubmed: 22716043
Nature. 2020 Sep;585(7825):357-362
pubmed: 32939066
J Cheminform. 2016 May 18;8:27
pubmed: 27195023
J Med Chem. 2003 Feb 13;46(4):499-511
pubmed: 12570372
J Mol Biol. 2016 Jun 5;428(11):2430-2445
pubmed: 27091468
J Cheminform. 2019 Aug 7;11(1):52
pubmed: 31392430
J Comput Aided Mol Des. 2019 Dec;33(12):1057-1069
pubmed: 31598897
J Comput Aided Mol Des. 2016 Sep;30(9):651-668
pubmed: 27696240
J Cheminform. 2020 May 27;12(1):37
pubmed: 33430966
Bioinformatics. 2019 Oct 1;35(19):3836-3838
pubmed: 30825370
Protein Sci. 2016 Jan;25(1):295-301
pubmed: 26103917
J Comput Aided Mol Des. 2019 Dec;33(12):1011-1020
pubmed: 31691919
J Chem Inf Model. 2014 Aug 25;54(8):2371-9
pubmed: 24931227
J Med Chem. 2012 Jan 26;55(2):623-38
pubmed: 22148468
J Med Chem. 2017 Nov 22;60(22):9400-9406
pubmed: 28929751
PLoS One. 2016 May 12;11(5):e0155183
pubmed: 27171006
J Comput Chem. 2007 Apr 30;28(6):1145-52
pubmed: 17274016
J Chem Inf Model. 2013 Mar 25;53(3):592-600
pubmed: 23394072
J Comput Aided Mol Des. 2020 Feb;34(2):99-119
pubmed: 31974851
J Med Chem. 2004 Mar 25;47(7):1739-49
pubmed: 15027865
Nat Protoc. 2016 May;11(5):905-19
pubmed: 27077332
J Mol Biol. 1996 Aug 23;261(3):470-89
pubmed: 8780787
J Comput Chem. 2017 Jan 30;38(3):169-177
pubmed: 27859414
J Chem Inf Model. 2013 Aug 26;53(8):1893-904
pubmed: 23379370
J Chem Inf Model. 2020 Jan 27;60(1):204-211
pubmed: 31887035
Molecules. 2015 May 29;20(6):9977-93
pubmed: 26035098
PLoS Comput Biol. 2015 Dec 02;11(12):e1004586
pubmed: 26629955
J Chem Inf Model. 2013 Feb 25;53(2):384-90
pubmed: 23351099
J Chem Inf Model. 2007 Jul-Aug;47(4):1481-92
pubmed: 17585754
J Comput Chem. 2010 Jan 30;31(2):455-61
pubmed: 19499576
J Chem Phys. 2012 Jul 28;137(4):044101
pubmed: 22852591
J Chem Theory Comput. 2021 Feb 9;17(2):1060-1073
pubmed: 33403848
J Chem Theory Comput. 2016 Feb 9;12(2):892-901
pubmed: 26744922
J Chem Inf Model. 2018 Aug 27;58(8):1697-1706
pubmed: 29989806
J Comput Aided Mol Des. 2019 Dec;33(12):1071-1081
pubmed: 31691920
Molecules. 2016 Nov 23;21(11):
pubmed: 27886114
Bioinformatics. 2015 Jul 1;31(13):2214-6
pubmed: 25717194
J Med Chem. 2005 Apr 7;48(7):2325-35
pubmed: 15801826
J Comput Aided Mol Des. 2002 Jan;16(1):11-26
pubmed: 12197663
J Cheminform. 2016 Oct 17;8:56
pubmed: 27803745
J Comput Chem. 2015 Jun 5;36(15):1132-56
pubmed: 25914306