SmartGraph: a network pharmacology investigation platform.
Bioactivity prediction
Network perturbation
Network pharmacology
Network visualization
Pathway analysis
Potent chemical pattern
Protein–protein interactions (PPIs)
Scaffold
Target deconvolution
neo4j
Journal
Journal of cheminformatics
ISSN: 1758-2946
Titre abrégé: J Cheminform
Pays: England
ID NLM: 101516718
Informations de publication
Date de publication:
21 Jan 2020
21 Jan 2020
Historique:
received:
23
07
2019
accepted:
07
01
2020
entrez:
12
1
2021
pubmed:
13
1
2021
medline:
13
1
2021
Statut:
epublish
Résumé
Drug discovery investigations need to incorporate network pharmacology concepts while navigating the complex landscape of drug-target and target-target interactions. This task requires solutions that integrate high-quality biomedical data, combined with analytic and predictive workflows as well as efficient visualization. SmartGraph is an innovative platform that utilizes state-of-the-art technologies such as a Neo4j graph-database, Angular web framework, RxJS asynchronous event library and D3 visualization to accomplish these goals. The SmartGraph framework integrates high quality bioactivity data and biological pathway information resulting in a knowledgebase comprised of 420,526 unique compound-target interactions defined between 271,098 unique compounds and 2018 targets. SmartGraph then performs bioactivity predictions based on the 63,783 Bemis-Murcko scaffolds extracted from these compounds. Through several use-cases, we illustrate the use of SmartGraph to generate hypotheses for elucidating mechanism-of-action, drug-repurposing and off-target prediction. https://smartgraph.ncats.io/.
Identifiants
pubmed: 33430980
doi: 10.1186/s13321-020-0409-9
pii: 10.1186/s13321-020-0409-9
pmc: PMC6974502
doi:
Types de publication
Journal Article
Langues
eng
Pagination
5Subventions
Organisme : NIH HHS
ID : 1U54CA189205-01
Pays : United States
Organisme : NIH HHS
ID : GM095952
Pays : United States
Références
J Cheminform. 2013 Jan 24;5(1):7
pubmed: 23343401
J Cheminform. 2019 Jul 10;11(1):47
pubmed: 31292807
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52
pubmed: 25352553
Algorithms Mol Biol. 2009 Oct 19;4:12
pubmed: 19840391
Bioinformatics. 2013 Oct 15;29(20):2655-6
pubmed: 23918250
Nucleic Acids Res. 2014 Jan;42(Database issue):D1083-90
pubmed: 24214965
Mol Inform. 2011 Mar 14;30(2-3):100-111
pubmed: 22287994
Nat Rev Drug Discov. 2018 May;17(5):317-332
pubmed: 29472638
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Nucleic Acids Res. 2012 Jan;40(Database issue):D1100-7
pubmed: 21948594
J Med Chem. 1996 Jul 19;39(15):2887-93
pubmed: 8709122
F1000Res. 2017 Jan 20;6:58
pubmed: 28413614
Nucleic Acids Res. 2011 Jan;39(Database issue):D367-72
pubmed: 20935044
Nat Biotechnol. 2007 Oct;25(10):1110-1
pubmed: 17921993
Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8
pubmed: 18084021
Nucleic Acids Res. 2016 Jan 4;44(D1):D548-54
pubmed: 26467481
Nucleic Acids Res. 2017 Jan 4;45(D1):D995-D1002
pubmed: 27903890
J Cheminform. 2018 Aug 20;10(1):41
pubmed: 30128806
J Med Chem. 2005 May 5;48(9):3182-93
pubmed: 15857124
J Cheminform. 2016 Mar 30;8:16
pubmed: 27030802
Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11473-8
pubmed: 16864780
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622