Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange' (doi:10.18419/darus-2109)

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

doi:10.18419/darus-2109

DaRUS

2022-01-16

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Markthaler, Daniel; Kraus, Hamzeh; Hansen, Niels, 2022, "Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'", https://doi.org/10.18419/darus-2109, DaRUS, V1

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

doi:10.18419/darus-2109

Markthaler, Daniel (Universität Stuttgart)

Kraus, Hamzeh (Universität Stuttgart)

Hansen, Niels (Universität Stuttgart)

EXC 2075 - 390740016

DaRUS

Hansen, Niels

Kraus, Hamzeh

2021-08-04

https://doi.org/10.18419/darus-2109

Chemistry, Physics, Molecular Dynamics Simulation, SAMPL8, Umbrella Sampling, Host-Guest Complex

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.

Input files for molecular dynamics simulations with GROMACS.

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).

10.1007/s10822-021-00439-w

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).

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FreeEnergyProfiles.tar.gz

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Collection of free energy profiles from US simulations (SAMPL8 challenge and training set)

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FreeEnergyProfiles_Chargescheme.pdf

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Free energy profiles from US simulations for ligands G1 and GT1 based upon different charge schemes

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FreeEnergyProfiles_SAMPL8.pdf

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Plot of free energy profiles from US simulations for ligand set of SAMPL8 challenge complexed with CB8

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FreeEnergyProfiles_TrainingSet.pdf

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Plot of free energy profiles from US simulations for ligand training set complexed with CB8

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G1_deprotonated.gro

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Cartesian coordinates of the guest molecule G1 in the deprotonated state in .gro format.

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G1_protonated.gro

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Cartesian coordinates of the guest molecule G1 in the protonated state in .gro format.

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G2_deprotonated.gro

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Cartesian coordinates of the guest molecule G2 in the deprotonated state in .gro format.

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G2_protonated.gro

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Cartesian coordinates of the guest molecule G2 in the protonated state in .gro format.

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G3_deprotonated.gro

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Cartesian coordinates of the guest molecule G3 in the deprotonated state in .gro format.

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G3_protonated.gro

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Cartesian coordinates of the guest molecule G3 in the protonated state in .gro format.

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G4_deprotonated.gro

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Cartesian coordinates of the guest molecule G4 in the deprotonated state in .gro format.

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G4_protonated.gro

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Cartesian coordinates of the guest molecule G4 in the protonated state in .gro format.

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G5_deprotonated_R-enantiomer.gro

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Cartesian coordinates of the R-enantiomer of the guest molecule G5 in the deprotonated state in .gro format.

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G5_deprotonated_S-enantiomer.gro

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Cartesian coordinates of the S-enantiomer of the guest molecule G5 in the deprotonated state in .gro format.

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G5_protonated_R-enantiomer.gro

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Cartesian coordinates of the R-enantiomer of the guest molecule G5 in the protonated state in .gro format.

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G5_protonated_S-enantiomer.gro

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Cartesian coordinates of the S-enantiomer of the guest molecule G5 in the protonated state in .gro format.

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G6_deprotonated.gro

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Cartesian coordinates of the guest molecule G6 in the deprotonated state in .gro format.

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G6_protonated.gro

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Cartesian coordinates of the guest molecule G6 in the protonated state in .gro format.

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G7_deprotonated.gro

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Cartesian coordinates of the guest molecule G7 in the deprotonated state in .gro format.

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G7_protonated.gro

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Cartesian coordinates of the guest molecule G7 in the protonated state in .gro format.

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GT1_deprotonated.gro

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Cartesian coordinates of the guest molecule GT1 in the deprotonated state in .gro format.

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GT1_protonated.gro

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Cartesian coordinates of the guest molecule GT1 in the protonated state in .gro format.

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GT2_deprotonated.gro

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Cartesian coordinates of the guest molecule GT2 in the deprotonated state in .gro format.

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GT2_protonated.gro

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Cartesian coordinates of the guest molecule GT2 in the protonated state in .gro format.

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GT3_deprotonated.gro

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Cartesian coordinates of the guest molecule GT3 in the deprotonated state in .gro format.

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GT3_protonated.gro

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Cartesian coordinates of the guest molecule GT3 in the protonated state in .gro format.

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GT4_deprotonated.gro

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Cartesian coordinates of the guest molecule GT4 in the deprotonated state in .gro format.

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GT4_protonated.gro

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Cartesian coordinates of the guest molecule GT4 in the protonated state in .gro format.

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GT5_deprotonated.gro

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Cartesian coordinates of the guest molecule GT5 in the deprotonated state in .gro format.

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GT5_protonated.gro

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Cartesian coordinates of the guest molecule GT5 in the protonated state in .gro format.

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CB7.gro

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Cartesian coordinates of the host molecule CB7 in .gro format.

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CB8.gro

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Cartesian coordinates of the host molecule CB8 in .gro format.

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G1_deprotonated.top

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Topology file of the guest molecule G1 in the deprotonated state in .top format.

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G1_protonated.top

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Topology file of the guest molecule G1 in the protonated state in .top format.

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G2_deprotonated.top

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Topology file of the guest molecule G2 in the deprotonated state in .top format.

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G2_protonated.top

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Topology file of the guest molecule G2 in the protonated state in .top format.

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G3_deprotonated.top

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Topology file of the guest molecule G3 in the deprotonated state in .top format.

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G3_protonated.top

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Topology file of the guest molecule G3 in the protonated state in .top format.

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G4_deprotonated.top

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Topology file of the guest molecule G4 in the deprotonated state in .top format.

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G4_protonated.top

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Topology file of the guest molecule G4 in the protonated state in .top format.

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G5_deprotonated_R-enantiomer.top

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Topology file of the R-enantiomer of the guest molecule G5 in the deprotonated state in .top format.

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G5_deprotonated_S-enantiomer.top

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Topology file of the S-enantiomer of the guest molecule G5 in the deprotonated state in .top format.

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G5_protonated_R-enantiomer.top

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Topology file of the R-enantiomer of the guest molecule G5 in the protonated state in .top format.

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G5_protonated_S-enantiomer.top

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Topology file of the S-enantiomer of the guest molecule G5 in the protonated state in .top format.

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G6_deprotonated.top

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Topology file of the guest molecule G6 in the deprotonated state in .top format.

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G6_protonated.top

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Topology file of the guest molecule G6 in the protonated state in .top format.

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G7_deprotonated.top

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Topology file of the guest molecule G7 in the deprotonated state in .top format.

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G7_protonated.top

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Topology file of the guest molecule G7 in the protonated state in .top format.

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GT1_deprotonated.top

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Topology file of the guest molecule GT1 in the deprotonated state in .top format.

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GT1_protonated.top

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Topology file of the guest molecule GT1 in the protonated state in .top format.

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GT2_deprotonated.top

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Topology file of the guest molecule GT2 in the deprotonated state in .top format.

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GT2_protonated.top

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Topology file of the guest molecule GT2 in the protonated state in .top format.

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GT3_deprotonated.top

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Topology file of the guest molecule GT3 in the deprotonated state in .top format.

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GT3_protonated.top

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Topology file of the guest molecule GT3 in the protonated state in .top format.

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GT4_deprotonated.top

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Topology file of the guest molecule GT4 in the deprotonated state in .top format.

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GT4_protonated.top

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Topology file of the guest molecule GT4 in the protonated state in .top format.

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GT5_deprotonated.top

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Topology file of the guest molecule GT5 in the deprotonated state in .top format.

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GT5_protonated.top

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Topology file of the guest molecule GT5 in the protonated state in .top format.

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CB7.top

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Topology file of the host molecule CB7 in .top format.

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CB8.top

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Topology file of the host molecule CB8 in .top format.

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