PASSer: Prediction of Allosteric Sites Server.
Journal
Machine learning: science and technology
ISSN: 2632-2153
Titre abrégé: Mach Learn Sci Technol
Pays: England
ID NLM: 101774789
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
entrez:
16
8
2021
pubmed:
17
8
2021
medline:
17
8
2021
Statut:
ppublish
Résumé
Allostery is considered important in regulating protein's activity. Drug development depends on the understanding of allosteric mechanisms, especially the identification of allosteric sites, which is a prerequisite in drug discovery and design. Many computational methods have been developed for allosteric site prediction using pocket features and protein dynamics. Here, we present an ensemble learning method, consisting of eXtreme gradient boosting (XGBoost) and graph convolutional neural network (GCNN), to predict allosteric sites. Our model can learn physical properties and topology without any
Identifiants
pubmed: 34396127
doi: 10.1088/2632-2153/abe6d6
pmc: PMC8360383
mid: NIHMS1728087
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : NIGMS NIH HHS
ID : R15 GM122013
Pays : United States
Références
Elife. 2016 Jan 12;5:e11860
pubmed: 26754770
J Chem Inf Model. 2017 Sep 25;57(9):2358-2363
pubmed: 28825477
Annu Rev Pharmacol Toxicol. 2014;54:165-84
pubmed: 24111540
Nucleic Acids Res. 2011 Jan;39(Database issue):D663-9
pubmed: 21051350
Nucleic Acids Res. 2015 Jan;43(Database issue):D399-404
pubmed: 25300483
Bioinformatics. 2015 Aug 1;31(15):2598-600
pubmed: 25810427
Bioinformatics. 2014 May 1;30(9):1314-5
pubmed: 24413526
Mol Pharm. 2019 Jun 3;16(6):2605-2615
pubmed: 31013097
Science. 2010 Feb 5;327(5966):653-4
pubmed: 20133562
J Comput Chem. 2018 Jul 30;39(20):1481-1490
pubmed: 29604117
J Chem Inf Model. 2019 Oct 28;59(10):4131-4149
pubmed: 31580672
Chem Sci. 2019 Jul 22;10(36):8438-8446
pubmed: 31803423
Proteins. 2008 Mar;70(4):1125-32
pubmed: 18076026
Chem Sci. 2018 Nov 26;10(2):370-377
pubmed: 30746086
Nat Commun. 2016 Aug 26;7:12477
pubmed: 27561351
Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11277-82
pubmed: 20534570
BMC Bioinformatics. 2009 Jun 02;10:168
pubmed: 19486540
Nucleic Acids Res. 2019 Jan 8;47(D1):D464-D474
pubmed: 30357411
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
J Comput Aided Mol Des. 2000 May;14(4):383-401
pubmed: 10815774
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W266-72
pubmed: 23737445
Nature. 2014 Apr 17;508(7496):331-9
pubmed: 24740064
Bioinformatics. 2013 Sep 15;29(18):2357-9
pubmed: 23842804
BMC Bioinformatics. 2012 Oct 25;13:273
pubmed: 23095452
J Chem Theory Comput. 2012 Aug 14;8(8):2962-71
pubmed: 26592133
J Am Chem Soc. 2014 Aug 20;136(33):11556-65
pubmed: 25061983
BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):381
pubmed: 32938395
Trends Pharmacol Sci. 2011 Dec;32(12):686-93
pubmed: 21925743
J Bioinform Comput Biol. 2018 Aug;16(4):1850014
pubmed: 30060698
J Chem Inf Model. 2017 Jun 26;57(6):1359-1374
pubmed: 28505454
BMC Bioinformatics. 2015 Oct 23;16:335
pubmed: 26493317
Mol Inform. 2016 Apr;35(3-4):125-35
pubmed: 27491922
J Phys Chem B. 2020 Oct 15;124(41):8960-8972
pubmed: 32970438
BMC Struct Biol. 2006 Sep 24;6:19
pubmed: 16995956