MolMeDB: Molecules on Membranes Database

Jakub Juračka, Martin Šrejber, Michaela Melíková, Václav Bazgier, Karel Berka
2019 Zenodo  
Biological membranes act as barriers or reservoirs for many compounds within a human body. They play an important role in the pharmacokinetics of drugs and other molecular species. Until now, most membrane/drug interactions are still inferred from simple partitioning between octanol and water phases. However, the variability among membrane composition and among compounds themselves is beyond such simplification as there are multiple drug-membrane interactions [1]. Nowadays there are also
more » ... ere are also numerous experimental and theoretical approaches on how to obtain them with variable accuracy, but there is no resource for their critical comparison. For this reason, we have built "Molecules on Membranes Database" (MolMeDB)[2] that collects data about compound-membrane interactions including partitioning, penetration, and free energy profiles of drug crossing the membrane along the membrane normal (Figure 1). Input info is collected from scientific articles published in peer-review journals and we added our inhouse calculations of free energy profiles and relevant partitioning and penetration properties from high-throughput COSMOmic [3] approach to set up a baseline for further comparison. Data in the MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method, or dataset and we offer collected data openly for further reuse. MolMeDB ( is a powerful tool for a better comparison of individual approaches used for the study of molecule/membrane interactions and for the community to evaluate the role of membranes in pharmacology.
doi:10.5281/zenodo.3560329 fatcat:xp4f6ckm3fgyjpaszw3pjhfkua