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MolMeDB: Molecules on Membranes Database

Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning betw...

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Autores principales: Juračka, Jakub, Šrejber, Martin, Melíková, Michaela, Bazgier, Václav, Berka, Karel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597476/
https://www.ncbi.nlm.nih.gov/pubmed/31250015
http://dx.doi.org/10.1093/database/baz078
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author Juračka, Jakub
Šrejber, Martin
Melíková, Michaela
Bazgier, Václav
Berka, Karel
author_facet Juračka, Jakub
Šrejber, Martin
Melíková, Michaela
Bazgier, Václav
Berka, Karel
author_sort Juračka, Jakub
collection PubMed
description Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug–membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule–membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound–membrane interactions including partitioning, penetration and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by in-house calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.
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spelling pubmed-65974762019-07-03 MolMeDB: Molecules on Membranes Database Juračka, Jakub Šrejber, Martin Melíková, Michaela Bazgier, Václav Berka, Karel Database (Oxford) Original Article Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug–membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule–membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound–membrane interactions including partitioning, penetration and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by in-house calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions. Oxford University Press 2019-06-27 /pmc/articles/PMC6597476/ /pubmed/31250015 http://dx.doi.org/10.1093/database/baz078 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Juračka, Jakub
Šrejber, Martin
Melíková, Michaela
Bazgier, Václav
Berka, Karel
MolMeDB: Molecules on Membranes Database
title MolMeDB: Molecules on Membranes Database
title_full MolMeDB: Molecules on Membranes Database
title_fullStr MolMeDB: Molecules on Membranes Database
title_full_unstemmed MolMeDB: Molecules on Membranes Database
title_short MolMeDB: Molecules on Membranes Database
title_sort molmedb: molecules on membranes database
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597476/
https://www.ncbi.nlm.nih.gov/pubmed/31250015
http://dx.doi.org/10.1093/database/baz078
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