Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins.
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 03 2020
23 03 2020
Historique:
pubmed:
8
1
2020
medline:
22
6
2021
entrez:
8
1
2020
Statut:
ppublish
Résumé
This article introduces Web-ARM, a specialized tool, online available, designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows the rapidly building of models of rhodopsins with a documented quality and the prediction of trends in UV-vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based
Identifiants
pubmed: 31909998
doi: 10.1021/acs.jcim.9b00615
pmc: PMC7101466
mid: NIHMS1560632
doi:
Substances chimiques
Rhodopsin
9009-81-8
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1481-1493Subventions
Organisme : NIGMS NIH HHS
ID : R15 GM126627
Pays : United States
Références
Biochemistry. 2009 May 26;48(20):4324-30
pubmed: 19334675
J Chem Theory Comput. 2012 Oct 9;8(10):3463-72
pubmed: 26592996
Science. 2018 Jul 13;361(6398):
pubmed: 29903883
BMC Bioinformatics. 2009 Jun 02;10:168
pubmed: 19486540
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
J Phys Chem B. 2018 May 10;122(18):4784-4792
pubmed: 29708342
Proteins. 2009 Dec;77(4):778-95
pubmed: 19603484
J Chem Theory Comput. 2013 Dec 10;9(12):5653-5674
pubmed: 24489522
J Chem Theory Comput. 2019 Aug 13;15(8):4535-4546
pubmed: 31264415
J Chem Theory Comput. 2016 Dec 13;12(12):6020-6034
pubmed: 27779842
J Chem Theory Comput. 2014 Jun 10;10(6):2232-45
pubmed: 26580747
J Chem Theory Comput. 2017 Sep 12;13(9):4003-4011
pubmed: 28723224
J Phys Chem Lett. 2019 Oct 17;10(20):6293-6300
pubmed: 31545053
Annu Rev Cell Dev Biol. 2000;16:365-92
pubmed: 11031241
J Biol Chem. 2004 Apr 16;279(16):16403-9
pubmed: 14757760
J Chem Theory Comput. 2019 Jan 8;15(1):775-786
pubmed: 30525595
J Chem Theory Comput. 2017 Dec 12;13(12):6391-6404
pubmed: 29112449
Biophys J. 1994 Sep;67(3):1187-91
pubmed: 7811932
J Chem Theory Comput. 2019 May 14;15(5):3134-3152
pubmed: 30916955
J Comput Chem. 2016 Feb 15;37(5):506-41
pubmed: 26561362
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
Bioinformatics. 2013 Apr 1;29(7):845-54
pubmed: 23407358
J Chem Inf Model. 2015 Feb 23;55(2):207-13
pubmed: 25629725
J Chem Theory Comput. 2019 Mar 12;15(3):2022-2032
pubmed: 30758952
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7
pubmed: 15215472
J Chem Inf Model. 2017 Sep 25;57(9):2161-2172
pubmed: 28812890
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5
pubmed: 17488841
J Chem Inf Model. 2018 Nov 26;58(11):2343-2354
pubmed: 30278128
PLoS One. 2013 Sep 06;8(9):e74092
pubmed: 24058518
J Chem Inf Model. 2017 Jul 24;57(7):1511-1516
pubmed: 28594549
Phys Chem Chem Phys. 2012 Sep 28;14(36):12485-95
pubmed: 22699180
Faraday Discuss. 2018 Apr 17;207(0):55-75
pubmed: 29388996
Chem Rev. 2014 Jan 8;114(1):126-63
pubmed: 24364740
Nat Commun. 2019 Apr 30;10(1):1993
pubmed: 31040285
J Chem Theory Comput. 2018 Apr 10;14(4):1823-1827
pubmed: 29506385
PLoS One. 2012;7(10):e45379
pubmed: 23056201
J Am Chem Soc. 2019 Jan 9;141(1):262-271
pubmed: 30532962
Mol Membr Biol. 2006 Mar-Apr;23(2):127-35
pubmed: 16754356
Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1714-9
pubmed: 24449866
Science. 2012 Sep 7;337(6099):1225-8
pubmed: 22955833
Biophys J. 1996 Dec;71(6):3392-8
pubmed: 8968608
Science. 2004 Nov 19;306(5700):1390-3
pubmed: 15459346
J Chem Theory Comput. 2011 Feb 8;7(2):525-37
pubmed: 26596171