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
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

5

Subventions

Organisme : NIH HHS
ID : 1U54CA189205-01
Pays : United States
Organisme : NIH HHS
ID : GM095952
Pays : United States

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Auteurs

Gergely Zahoránszky-Kőhalmi (G)

National Center for Advancing Translational Sciences, Rockville, MD, USA. gzahoranszky@gmail.com.
Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA. gzahoranszky@gmail.com.

Timothy Sheils (T)

National Center for Advancing Translational Sciences, Rockville, MD, USA.

Tudor I Oprea (TI)

Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA.
UNM Comprehensive Cancer Center, Albuquerque, NM, USA.
Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy At University of Gothenburg, Gothenburg, Sweden.
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Classifications MeSH