Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations

Christian Hoffmann, Alessia Centi, Roberto Menichetti, Tristan Bereau
2020 Scientific Data  
The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes-exhaustively enumerating all 105
more » ... CG dimers-and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.
doi:10.1038/s41597-020-0391-0 pmid:32054852 pmcid:PMC7018832 fatcat:ottf4v4n3zfnjacc6iibheztpq