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Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase

The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we exten...

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Detalles Bibliográficos
Autores principales: Vinhoven, Liza, Voskamp, Malte, Nietert, Manuel Manfred
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8625161/
https://www.ncbi.nlm.nih.gov/pubmed/34834423
http://dx.doi.org/10.3390/jpm11111072
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author Vinhoven, Liza
Voskamp, Malte
Nietert, Manuel Manfred
author_facet Vinhoven, Liza
Voskamp, Malte
Nietert, Manuel Manfred
author_sort Vinhoven, Liza
collection PubMed
description The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA’s own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online.
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spelling pubmed-86251612021-11-27 Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase Vinhoven, Liza Voskamp, Malte Nietert, Manuel Manfred J Pers Med Article The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA’s own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online. MDPI 2021-10-24 /pmc/articles/PMC8625161/ /pubmed/34834423 http://dx.doi.org/10.3390/jpm11111072 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Vinhoven, Liza
Voskamp, Malte
Nietert, Manuel Manfred
Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase
title Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase
title_full Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase
title_fullStr Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase
title_full_unstemmed Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase
title_short Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase
title_sort mapping compound databases to disease maps—a minerva plugin for candactbase
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8625161/
https://www.ncbi.nlm.nih.gov/pubmed/34834423
http://dx.doi.org/10.3390/jpm11111072
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