Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
13 02 2020
13 02 2020
Historique:
received:
07
10
2019
accepted:
22
01
2020
entrez:
15
2
2020
pubmed:
15
2
2020
medline:
21
10
2020
Statut:
epublish
Résumé
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 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.
Identifiants
pubmed: 32054852
doi: 10.1038/s41597-020-0391-0
pii: 10.1038/s41597-020-0391-0
pmc: PMC7018832
doi:
Substances chimiques
Pharmaceutical Preparations
0
Types de publication
Dataset
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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