Data · dataset · 2022
Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Listed in DaRUS
Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the recent SAMPL8 CB8 "Drugs of Abuse" challenge using the GROMACS MD package.
Description
To compare with experimental data, a scheme for correcting the raw simulation estimates was proposed in the related publication on the basis of five training molecules (GT1-GT5) with experimentally known binding affinities towards CB8.
The deposited dataset contains coordinates and molecular topologies in GROMACS format as well as free energy profiles accompanying the related publication. For each guest molecule, two protonation states were simulated (protonated, deprotonated) and for one of the drugs, G5, both of its enantiomeric forms (R, S) were considered.
Links
Where it is published
- Dataverse dataset page darus.uni-stuttgart.de/dataset.xhtml?persistentId=doi%3A10.18419%2FDARUS-2109 ↗
landing page · from darus uni stuttgart de
- DOI doi.org/10.18419/darus-2109 ↗
DOI / persistent id · from darus uni stuttgart de
Catalogue records · 1
- Dataverse API darus.uni-stuttgart.de/api/datasets/:persistentId/?persistentId=doi%3A10.18419%2FDARU… ↗
metadata API · from darus uni stuttgart de
Topics
- From keywords
- Chemistry · Life Sciences · Physics
- Inferred from text
- Cheminformatics and quantitative structure-activity relationships 80% · Simulation 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DaRUS | doi:10.18419/DARUS-2109 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:field:340404 | enrichment · darus uni stuttgart de | taxonomy-embedding@1.1.0 | title+keywords+description (80%) |
| concepts[field].dataverse_subject:chemistry | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[field].dataverse_subject:physics | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[field].local:field:physics | mapping · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /subjects |
| concepts[method].local:method:simulation | enrichment · darus uni stuttgart de | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | |
| description | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /description |
| publication_date | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | |
| title | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | /name |
| updated_date | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 | |
| version_label | source · darus uni stuttgart de | connector:darus_uni_stuttgart_de@1.0.0 |