Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'

DOI

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. 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.

Identifier
DOI https://doi.org/10.18419/darus-2109
Related Identifier IsCitedBy https://doi.org/10.1007/s10822-021-00439-w
Metadata Access https://darus.uni-stuttgart.de/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.18419/darus-2109
Provenance
Creator Markthaler, Daniel (ORCID: 0000-0003-3281-436X); Kraus, Hamzeh ORCID logo; Hansen, Niels ORCID logo
Publisher DaRUS
Contributor Hansen, Niels
Publication Year 2022
Funding Reference Deutsche Forschungsgemeinschaft EXC 2075 - 390740016
Rights CC BY 4.0; info:eu-repo/semantics/openAccess; http://creativecommons.org/licenses/by/4.0
OpenAccess true
Contact Hansen, Niels (Universität Stuttgart)
Representation
Resource Type Input files for molecular dynamics simulations with GROMACS.; Dataset
Format application/octet-stream; application/pdf; application/x-gzip
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Version 1.0
Discipline Chemistry; Natural Sciences; Physics