%0 Generic %1 markthaler2022supplementary %A Markthaler, Daniel %A Kraus, Hamzeh %A Hansen, Niels %D 2022 %K darus mult ubs_10004 ubs_20005 ubs_20006 ubs_30058 ubs_30060 ubs_40084 unibibliografie %R 10.18419/darus-2109 %T Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange' %X Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit8uril, 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.

@misc{markthaler2022supplementary, abstract = {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.}, added-at = {2022-03-08T18:38:51.000+0100}, affiliation = {Markthaler, Daniel/Universität Stuttgart, Kraus, Hamzeh/Universität Stuttgart, Hansen, Niels/Universität Stuttgart}, author = {Markthaler, Daniel and Kraus, Hamzeh and Hansen, Niels}, biburl = {https://puma.ub.uni-stuttgart.de/bibtex/2dad78540d53bab6c226706031cedb9f3/unibiblio}, doi = {10.18419/darus-2109}, howpublished = {Dataset}, interhash = {3a98f245b635275f0a861d2ccdbbae35}, intrahash = {dad78540d53bab6c226706031cedb9f3}, keywords = {darus mult ubs_10004 ubs_20005 ubs_20006 ubs_30058 ubs_30060 ubs_40084 unibibliografie}, note = {Related to: D. Markthaler, H. Kraus, N. Hansen, Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange. In: Journal of Computer-Aided Molecular Design (2022). doi: 10.1007/s10822-021-00439-w}, orcid-numbers = {Markthaler, Daniel/0000-0003-3281-436X, Kraus, Hamzeh/0000-0001-9643-4839, Hansen, Niels/0000-0003-4366-6120}, timestamp = {2024-02-08T17:23:40.000+0100}, title = {Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'}, year = 2022 }