SmartGraph: a network pharmacology investigation platform
Abstract Motivation 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 wo...
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| Fformat: | Erthygl |
| Iaith: | English |
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BMC
2020-01-01
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| Cyfres: | Journal of Cheminformatics |
| Pynciau: | |
| Mynediad Ar-lein: | https://doi.org/10.1186/s13321-020-0409-9 |
| _version_ | 1831676081878335488 |
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| author | Gergely Zahoránszky-Kőhalmi Timothy Sheils Tudor I. Oprea |
| author_facet | Gergely Zahoránszky-Kőhalmi Timothy Sheils Tudor I. Oprea |
| author_sort | Gergely Zahoránszky-Kőhalmi |
| collection | DOAJ |
| description | Abstract Motivation 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. Results 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. Availability https://smartgraph.ncats.io/. |
| first_indexed | 2024-12-20T04:16:42Z |
| format | Article |
| id | doaj.art-7b92e30661424dbaa7d66cc8c29ece30 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-20T04:16:42Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-7b92e30661424dbaa7d66cc8c29ece302022-12-21T19:53:45ZengBMCJournal of Cheminformatics1758-29462020-01-0112111110.1186/s13321-020-0409-9SmartGraph: a network pharmacology investigation platformGergely Zahoránszky-Kőhalmi0Timothy Sheils1Tudor I. Oprea2National Center for Advancing Translational SciencesNational Center for Advancing Translational SciencesDepartment of Internal Medicine, University of New Mexico School of MedicineAbstract Motivation 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. Results 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. Availability https://smartgraph.ncats.io/.https://doi.org/10.1186/s13321-020-0409-9Network pharmacologyPathway analysisTarget deconvolutionNetwork perturbationProtein–protein interactions (PPIs)Bioactivity prediction |
| spellingShingle | Gergely Zahoránszky-Kőhalmi Timothy Sheils Tudor I. Oprea SmartGraph: a network pharmacology investigation platform Journal of Cheminformatics Network pharmacology Pathway analysis Target deconvolution Network perturbation Protein–protein interactions (PPIs) Bioactivity prediction |
| title | SmartGraph: a network pharmacology investigation platform |
| title_full | SmartGraph: a network pharmacology investigation platform |
| title_fullStr | SmartGraph: a network pharmacology investigation platform |
| title_full_unstemmed | SmartGraph: a network pharmacology investigation platform |
| title_short | SmartGraph: a network pharmacology investigation platform |
| title_sort | smartgraph a network pharmacology investigation platform |
| topic | Network pharmacology Pathway analysis Target deconvolution Network perturbation Protein–protein interactions (PPIs) Bioactivity prediction |
| url | https://doi.org/10.1186/s13321-020-0409-9 |
| work_keys_str_mv | AT gergelyzahoranszkykohalmi smartgraphanetworkpharmacologyinvestigationplatform AT timothysheils smartgraphanetworkpharmacologyinvestigationplatform AT tudorioprea smartgraphanetworkpharmacologyinvestigationplatform |