Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.
BioExcel
COVID19
exascale
molecular dynamics
Journal
Wiley interdisciplinary reviews. Computational molecular science
ISSN: 1759-0876
Titre abrégé: Wiley Interdiscip Rev Comput Mol Sci
Pays: United States
ID NLM: 101564639
Informations de publication
Date de publication:
30 May 2022
30 May 2022
Historique:
received:
02
02
2022
revised:
25
04
2022
accepted:
28
04
2022
entrez:
8
8
2022
pubmed:
9
8
2022
medline:
9
8
2022
Statut:
aheadofprint
Résumé
Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid-19 pandemics. This article is categorized under:Data Science > Computer Algorithms and ProgrammingData Science > Databases and Expert SystemsMolecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods.
Identifiants
pubmed: 35935573
doi: 10.1002/wcms.1622
pii: WCMS1622
pmc: PMC9347456
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e1622Informations de copyright
© 2022 Wiley Periodicals LLC.
Références
Structure. 2010 Nov 10;18(11):1399-409
pubmed: 21070939
ACS Cent Sci. 2020 Feb 26;6(2):189-196
pubmed: 32123736
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9193-8
pubmed: 27482115
J Comput Chem. 2015 Feb 15;36(5):348-54
pubmed: 25487359
J Chem Phys. 2016 Feb 21;144(7):075101
pubmed: 26897000
Angew Chem Int Ed Engl. 2016 Jun 20;55(26):7364-8
pubmed: 27122231
Nucleic Acids Res. 2019 Jan 8;47(D1):D390-D397
pubmed: 30418645
Nucleic Acids Res. 2019 Dec 2;47(21):11090-11102
pubmed: 31624840
J Chem Theory Comput. 2018 Dec 11;14(12):6175-6182
pubmed: 30407810
J Phys Chem B. 2021 May 6;125(17):4241-4261
pubmed: 33905257
Int J Mol Sci. 2021 Jul 19;22(14):
pubmed: 34299333
J Chem Phys. 2019 Dec 21;151(23):234113
pubmed: 31864270
Proc Natl Acad Sci U S A. 2021 May 11;118(19):
pubmed: 33883267
Nat Commun. 2021 Jun 15;12(1):3623
pubmed: 34131140
PLoS One. 2012;7(5):e33931
pubmed: 22606222
Annu Rev Biophys. 2017 May 22;46:43-57
pubmed: 28301772
J Biol Chem. 2021 Jul;297(1):100770
pubmed: 33989635
J Chem Theory Comput. 2020 Oct 13;16(10):6586-6597
pubmed: 32786900
J Chem Theory Comput. 2014 Feb 11;10(2):524-33
pubmed: 26580029
J Phys Chem B. 2011 Aug 4;115(30):9431-8
pubmed: 21714551
ACS Cent Sci. 2019 May 22;5(5):755-767
pubmed: 31139712
Biophys J. 2021 Mar 16;120(6):1072-1084
pubmed: 33189680
J Chem Theory Comput. 2016 Aug 9;12(8):3473-81
pubmed: 27340835
Mol Syst Des Eng. 2021 Nov 18;7(2):123-131
pubmed: 35223088
J Am Chem Soc. 2020 Dec 30;142(52):21883-21890
pubmed: 33320670
Wiley Interdiscip Rev Comput Mol Sci. 2022 May 30;:e1622
pubmed: 35935573
ACS Catal. 2020;10:12544-12554
pubmed: 34192089
J Chem Theory Comput. 2012 Nov 13;8(11):4707-18
pubmed: 26605625
Science. 2021 Aug 6;373(6555):
pubmed: 34168071
ACS Cent Sci. 2018 Dec 26;4(12):1708-1718
pubmed: 30648154
J Cheminform. 2020 Jun 1;12(1):40
pubmed: 33431029
Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10
pubmed: 27137889
Nat Rev Microbiol. 2021 Mar;19(3):155-170
pubmed: 33116300
Cell. 2020 Apr 16;181(2):281-292.e6
pubmed: 32155444
Gigascience. 2021 Jan 13;10(1):
pubmed: 33438730
Bioinformatics. 2013 May 15;29(10):1325-32
pubmed: 23479348
J Phys Chem B. 2008 Mar 20;112(11):3432-40
pubmed: 18290641
J Chem Phys. 2018 Nov 14;149(18):180901
pubmed: 30441927
Bioinformatics. 2012 Apr 15;28(8):1166-7
pubmed: 22368248
Chem Catal. 2022 May 19;2(5):1084-1099
pubmed: 35465139
J Chem Theory Comput. 2008 May 9;4(6):869-876
pubmed: 19936324
Lancet Infect Dis. 2020 Sep;20(9):1043-1050
pubmed: 32539988
Nature. 1977 Jun 16;267(5612):585-90
pubmed: 301613
Bioconjug Chem. 2017 Sep 20;28(9):2327-2339
pubmed: 28806062
PLoS Comput Biol. 2019 Jan 17;15(1):e1006649
pubmed: 30653494
Mol Inform. 2017 Oct;36(10):
pubmed: 28586180
Comput Phys Commun. 2014 Mar;185(3):908-916
pubmed: 24944348
Nucleic Acids Res. 2008 Apr;36(7):2379-94
pubmed: 18299282
Biophys J. 2004 Aug;87(2):800-11
pubmed: 15298889
Science. 2019 Sep 6;365(6457):
pubmed: 31488660
Angew Chem Int Ed Engl. 2010 Oct 11;49(42):7673-6
pubmed: 20845348
Biophys J. 2017 Jun 20;112(12):2469-2474
pubmed: 28636905
J Chem Theory Comput. 2018 Dec 11;14(12):6127-6138
pubmed: 30354113
Methods Mol Biol. 2019;1851:19-47
pubmed: 30298390
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995 Sep;52(3):2893-2906
pubmed: 9963736
Chem Sci. 2019 Dec 2;11(4):1140-1152
pubmed: 34084371
Curr Opin Struct Biol. 2015 Apr;31:64-74
pubmed: 25845770
J Phys Chem Lett. 2018 May 3;9(9):2144-2150
pubmed: 29630378
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
Science. 2020 May 8;368(6491):630-633
pubmed: 32245784
J Chem Theory Comput. 2015 Feb 10;11(2):800-9
pubmed: 26392815
Nat Commun. 2020 Jun 24;11(1):3202
pubmed: 32581217
Sci Adv. 2021 Apr 16;7(16):
pubmed: 33863729
Biophys J. 2021 Mar 16;120(6):1097-1104
pubmed: 33253634
Science. 1987 May 1;236(4801):564-8
pubmed: 3576184
Nature. 2020 Nov;587(7835):657-662
pubmed: 32726803
J Virol. 2011 May;85(9):4122-34
pubmed: 21325420
Proc Natl Acad Sci U S A. 2021 May 11;118(19):
pubmed: 33903171
Nat Commun. 2016 Apr 04;7:10910
pubmed: 27040077
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Sep;60(3):2721-6
pubmed: 11970075
J Chem Inf Model. 2017 Feb 27;57(2):109-114
pubmed: 28181802
Life Sci. 2020 Sep 15;257:118056
pubmed: 32645344
Brief Bioinform. 2017 May 1;18(3):530-536
pubmed: 27013646
Front Immunol. 2020 Oct 07;11:576622
pubmed: 33117378
J Comput Chem. 2008 Aug;29(11):1859-65
pubmed: 18351591
Bioinformatics. 2004 Nov 22;20(17):3045-54
pubmed: 15201187
ACS Pharmacol Transl Sci. 2021 Mar 16;4(3):1079-1095
pubmed: 34136757
J Virol. 2010 Dec;84(24):12658-64
pubmed: 20926566
Interface Focus. 2021 Oct 12;11(6):20210018
pubmed: 34956592
Bioinformatics. 2016 Nov 1;32(21):3371-3373
pubmed: 27354697
Cell Rep. 2021 Jan 12;34(2):108630
pubmed: 33417835
Nucleic Acids Res. 2017 Apr 20;45(7):4217-4230
pubmed: 28088759
Nature. 2020 Dec;588(7836):E6
pubmed: 33199918
J Comput Chem. 2019 Oct 15;40(27):2418-2431
pubmed: 31260119
Biol Direct. 2015 Aug 19;10:43
pubmed: 26282399
J Mol Biol. 1969 Dec 14;46(2):269-79
pubmed: 5360040
Comput Sci Eng. 2020 Nov 06;23(1):7-16
pubmed: 35939280
J Chem Theory Comput. 2012 May 8;8(5):1542-1555
pubmed: 22582031
Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17874-9
pubmed: 24128758
Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):796-801
pubmed: 17215349
J Mol Graph Model. 2010 Sep;29(2):116-25
pubmed: 20675161
J Chem Theory Comput. 2015 Dec 8;11(12):5747-57
pubmed: 26588361
Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12562-6
pubmed: 12271136
Nat Commun. 2017 Dec;8(1):6
pubmed: 28232750
J Chem Theory Comput. 2015 Feb 10;11(2):766-79
pubmed: 25691833
BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):482
pubmed: 30577753
Elife. 2020 Aug 19;9:
pubmed: 32812868
Bioinformatics. 2012 May 1;28(9):1278-9
pubmed: 22437851
Sci Data. 2019 Sep 10;6(1):169
pubmed: 31506435
Sci Adv. 2020 Sep 11;6(37):
pubmed: 32917717
J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475
pubmed: 30240203
Methods. 2010 Sep;52(1):99-105
pubmed: 20570730
J Phys Chem B. 2018 May 31;122(21):5389-5399
pubmed: 29401388
Nat Methods. 2018 Jul;15(7):475-476
pubmed: 29967506
Cell Mol Immunol. 2022 Feb;19(2):293-295
pubmed: 35017716
Science. 2020 Mar 27;367(6485):1444-1448
pubmed: 32132184
Gigascience. 2019 Nov 1;8(11):
pubmed: 31675414
J Chem Phys. 2020 Oct 7;153(13):134110
pubmed: 33032406
J Chem Theory Comput. 2016 Apr 12;12(4):1845-52
pubmed: 26949976
Nucleic Acids Res. 2014 Oct 29;42(19):12272-83
pubmed: 25260586
Nat Chem. 2021 Jul;13(7):651-659
pubmed: 34031561
J Comput Chem. 2021 Feb 5;42(4):231-241
pubmed: 33200457
Biochim Biophys Acta Biomembr. 2022 Oct 1;1864(10):183994
pubmed: 35724739
Nature. 2013 May 30;497(7451):643-6
pubmed: 23719463
Science. 2020 Mar 13;367(6483):1255-1260
pubmed: 32165587
Phys Rev Lett. 2008 Jan 18;100(2):020603
pubmed: 18232845
Sci Rep. 2017 Nov 15;7(1):15604
pubmed: 29142210
BMC Bioinformatics. 2013 Aug 22;14:257
pubmed: 24103053
Mol Inform. 2020 Aug;39(8):e2000028
pubmed: 32162456
Proc Natl Acad Sci U S A. 2021 Oct 26;118(43):
pubmed: 34615730
J Chem Theory Comput. 2014 May 13;10(5):2064-9
pubmed: 26580533
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13749-54
pubmed: 16172406
Glycobiology. 2021 May 3;31(4):410-424
pubmed: 33135055
ACS Cent Sci. 2020 Oct 28;6(10):1722-1734
pubmed: 33140034
PLoS Biol. 2015 Nov 24;13(11):e1002303
pubmed: 26600012
ACS Cent Sci. 2021 Jan 27;7(1):164-174
pubmed: 33527086
Structure. 2010 Mar 14;18(4):423-35
pubmed: 20399180
J Chem Theory Comput. 2015 Jan 13;11(1):2-7
pubmed: 26574197
Elife. 2018 Oct 05;7:
pubmed: 30289386
J Comput Aided Mol Des. 2012 Jul;26(7):801-4
pubmed: 22644661
J Chem Theory Comput. 2020 Dec 8;16(12):7915-7925
pubmed: 33170696
Sci Rep. 2021 Apr 1;11(1):7429
pubmed: 33795718
Nature. 2019 Jun;570(7759):27-29
pubmed: 31164768
J Comput Chem. 2014 Jan 30;35(3):260-9
pubmed: 24258850
J Phys Chem B. 2007 May 3;111(17):4553-9
pubmed: 17419610
J Chem Phys. 2006 Jul 14;125(2):24106
pubmed: 16848576
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W47-55
pubmed: 23685436
Sci Adv. 2020 Dec 9;6(50):
pubmed: 33158912
Nature. 2020 May;581(7807):215-220
pubmed: 32225176
Chem Sci. 2021 Feb 2;12(13):4889-4907
pubmed: 34168762
J Biol Chem. 2020 May 15;295(20):6785-6797
pubmed: 32284326
J Chem Phys. 2013 Jul 7;139(1):015102
pubmed: 23822324
Front Mol Biosci. 2020 Aug 28;7:194
pubmed: 33005628
Nucleic Acids Res. 2016 Jan 4;44(D1):D272-8
pubmed: 26612862
Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):E3221-30
pubmed: 27226302
Int J Mol Sci. 2020 Jul 28;21(15):
pubmed: 32731361