Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands.
Journal
Journal of chemical theory and computation
ISSN: 1549-9626
Titre abrégé: J Chem Theory Comput
Pays: United States
ID NLM: 101232704
Informations de publication
Date de publication:
13 Jul 2021
13 Jul 2021
Historique:
pubmed:
9
6
2021
medline:
9
6
2021
entrez:
8
6
2021
Statut:
ppublish
Résumé
In this work, the discrete λ variant of the Gibbs sampler-based λ-dynamics (
Identifiants
pubmed: 34101448
doi: 10.1021/acs.jctc.1c00176
pmc: PMC8627277
mid: NIHMS1759128
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
3895-3907Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM103695
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM037554
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM130587
Pays : United States
Organisme : NCRR NIH HHS
ID : R01 RR023920
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM107233
Pays : United States
Références
Phys Rev Lett. 2001 Mar 5;86(10):2050-3
pubmed: 11289852
Bioorg Med Chem. 2016 Oct 15;24(20):4768-4778
pubmed: 27485603
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
pubmed: 8744570
Phys Rev A Gen Phys. 1985 Mar;31(3):1695-1697
pubmed: 9895674
J Chem Phys. 2011 Nov 21;135(19):194110
pubmed: 22112069
J Chem Theory Comput. 2015 Mar 10;11(3):1267-77
pubmed: 26579773
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13749-54
pubmed: 16172406
J Comput Chem. 2012 Jan 15;33(2):189-202
pubmed: 22042689
J Comput Chem. 2004 Jul 15;25(9):1157-74
pubmed: 15116359
J Comput Chem. 2014 Feb 15;35(5):406-13
pubmed: 24302199
J Chem Theory Comput. 2009 Apr 14;5(4):919-30
pubmed: 26609601
Curr Opin Struct Biol. 2011 Apr;21(2):150-60
pubmed: 21349700
J Phys Chem Lett. 2018 Jun 21;9(12):3328-3332
pubmed: 29847134
J Comput Chem. 2020 Apr 15;41(10):986-999
pubmed: 31930547
Protein Sci. 2018 Nov;27(11):1910-1922
pubmed: 30175503
J Comput Chem. 2004 Oct;25(13):1605-12
pubmed: 15264254
J Chem Theory Comput. 2011 Sep 13;7(9):2728-2739
pubmed: 22125476
J Comput Chem. 2011 Dec;32(16):3423-32
pubmed: 21919014
J Comput Chem. 2010 Mar;31(4):671-90
pubmed: 19575467
J Chem Theory Comput. 2015 Jun 9;11(6):2575-88
pubmed: 26575556
J Chem Theory Comput. 2018 Nov 13;14(11):5567-5582
pubmed: 30289712
J Chem Theory Comput. 2014 Aug 12;10(8):3006-22
pubmed: 26588272
J Chem Theory Comput. 2014 Jul 8;10(7):2632-47
pubmed: 26586503
J Phys Chem B. 2018 May 17;122(19):5030-5037
pubmed: 29669415
J Chem Theory Comput. 2016 Jan 12;12(1):281-96
pubmed: 26584231
J Chem Theory Comput. 2017 Jun 13;13(6):2501-2510
pubmed: 28510433
J Chem Phys. 2007 Nov 14;127(18):184105
pubmed: 18020628
J Chem Theory Comput. 2011 Sep 13;7(9):2721-2727
pubmed: 22125475
J Chem Theory Comput. 2020 Dec 8;16(12):7895-7914
pubmed: 33201701
J Am Chem Soc. 2013 Nov 6;135(44):16705-13
pubmed: 24151856
J Comput Aided Mol Des. 2014 Jul;28(7):711-20
pubmed: 24928188
J Comput Chem. 2014 Jan 30;35(3):227-43
pubmed: 24249099
J Chem Theory Comput. 2015 Jul 14;11(7):3499-509
pubmed: 26190950
J Chem Inf Model. 2018 Oct 22;58(10):2043-2050
pubmed: 30199633
J Chem Theory Comput. 2013 Feb 12;9(2):909-26
pubmed: 26588735
J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092
pubmed: 30351006
J Comput Chem. 2009 Jul 30;30(10):1545-614
pubmed: 19444816
J Chem Inf Model. 2020 Nov 23;60(11):5457-5474
pubmed: 32813975
J Chem Inf Model. 2012 Dec 21;52(12):3144-54
pubmed: 23146088
J Chem Phys. 2007 May 14;126(18):184110
pubmed: 17508795
J Chem Theory Comput. 2021 Oct 12;17(10):6262-6280
pubmed: 34551262
J Chem Inf Model. 2020 Nov 23;60(11):5301-5307
pubmed: 32805108
J Comput Chem. 2019 Oct 15;40(27):2418-2431
pubmed: 31260119
J Chem Theory Comput. 2010 May 11;6(5):1509-19
pubmed: 26615687
J Chem Inf Model. 2020 Nov 23;60(11):5308-5318
pubmed: 32818371
J Phys Chem B. 2017 Apr 20;121(15):3864-3870
pubmed: 28224794
PLoS Comput Biol. 2017 Jul 26;13(7):e1005659
pubmed: 28746339
IEEE Trans Pattern Anal Mach Intell. 1984 Jun;6(6):721-41
pubmed: 22499653
J Chem Theory Comput. 2019 Feb 12;15(2):799-802
pubmed: 30689377
J Chem Theory Comput. 2009 Feb 10;5(2):350-358
pubmed: 20150953
J Phys Chem B. 2017 Apr 20;121(15):3626-3635
pubmed: 28112940
J Mol Graph Model. 2004 May;22(5):377-95
pubmed: 15099834
J Comput Chem. 2020 Jan 30;41(3):247-257
pubmed: 31721260
ACS Med Chem Lett. 2014 Oct 13;5(11):1259-62
pubmed: 25408842
J Comput Chem. 2009 Aug;30(11):1692-700
pubmed: 19421993
Science. 2004 Mar 19;303(5665):1813-8
pubmed: 15031495
J Chem Theory Comput. 2010 Jul 1;6(9):2559-2565
pubmed: 21857813
J Comput Aided Mol Des. 2013 Sep;27(9):755-70
pubmed: 24072356
J Chem Theory Comput. 2008 Oct 14;4(10):1565-1569
pubmed: 19461870
J Phys Chem B. 2010 Aug 19;114(32):10235-53
pubmed: 20701361
Entropy (Basel). 2018 May;20(5):
pubmed: 30393452
J Chem Inf Model. 2017 Dec 26;57(12):2911-2937
pubmed: 29243483
J Chem Theory Comput. 2013 Feb 12;9(2):1282-93
pubmed: 26588769
J Phys Chem Lett. 2019 Sep 5;10(17):4875-4880
pubmed: 31386370
J Chem Theory Comput. 2019 Apr 9;15(4):2392-2419
pubmed: 30821973
J Chem Phys. 2013 Nov 14;139(18):184103
pubmed: 24320250
J Chem Phys. 2008 Sep 28;129(12):124105
pubmed: 19045004
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273
pubmed: 23341755
J Chem Phys. 2014 Nov 28;141(20):201101
pubmed: 25429926
J Chem Phys. 2020 Sep 21;153(11):114502
pubmed: 32962378
J Chem Eng Data. 2017 May 11;62(5):1559-1569
pubmed: 29056756
Biophys J. 2012 Sep 5;103(5):1045-51
pubmed: 23009854
J Chem Theory Comput. 2009 Feb 10;5(2):276-86
pubmed: 26610104
J Chem Inf Model. 2020 Jun 22;60(6):3120-3130
pubmed: 32437145
J Chem Theory Comput. 2018 Dec 11;14(12):6346-6358
pubmed: 30375870
J Chem Theory Comput. 2017 Mar 14;13(3):1439-1453
pubmed: 28103438
J Chem Inf Model. 2019 Nov 25;59(11):4720-4728
pubmed: 31613620
J Chem Inf Model. 2012 Dec 21;52(12):3155-68
pubmed: 23145473
J Am Chem Soc. 2015 Feb 25;137(7):2695-703
pubmed: 25625324
Biopolymers. 1985 May;24(5):843-65
pubmed: 2410050
J Comput Aided Mol Des. 2012 Jan;26(1):93-5
pubmed: 22113833