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7,731 to 7,740 of 8,106 Results
trofy_350_11_1mus_7.5ns-p-s.mp4
Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica'
MPEG-4 Video - 1.0 GB - MD5: 604a66237b46765bbbd1a8e73d4714ec
MD Simulation trajectory of 1 mus simulated at 350 K of a Pore with 11 beta-CD molecules attached to the surface using the Trofymchuk linker with 30 benzene molecules in water. Hereby one video second corresponds to 7.5 ns.
Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Jan 16, 2022
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
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 propose...
CB7.gro
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Unknown - 5.6 KB - MD5: 09821d8211a26494894920b1b5d544b5
Cartesian coordinates of the host molecule CB7 in .gro format.
CB7.top
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Unknown - 81.9 KB - MD5: 9e220cac8149daef0465ee4e3f0399fb
Topology file of the host molecule CB7 in .top format.
CB8.gro
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Unknown - 6.4 KB - MD5: ecbaf94327d0ac6087a430301564c398
Cartesian coordinates of the host molecule CB8 in .gro format.
CB8.top
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Unknown - 93.2 KB - MD5: 5b340db669d8cd2d04ccefa1fe064ba8
Topology file of the host molecule CB8 in .top format.
FreeEnergyProfiles_Chargescheme.pdf
FreeEnergyProfiles_Chargescheme.pdf
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Adobe PDF - 21.3 KB - MD5: c2ee06a80c3f45654ca23c096a8bc632
Free energy profiles from US simulations for ligands G1 and GT1 based upon different charge schemes
FreeEnergyProfiles_SAMPL8.pdf
FreeEnergyProfiles_SAMPL8.pdf
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Adobe PDF - 29.8 KB - MD5: b3e3071f2ebe7bd1c2fc7c95ecf96778
Plot of free energy profiles from US simulations for ligand set of SAMPL8 challenge complexed with CB8
FreeEnergyProfiles.tar.gz
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Gzip Archive - 90.0 KB - MD5: df6de9be7258c97195002494d939a4e0
Collection of free energy profiles from US simulations (SAMPL8 challenge and training set)
FreeEnergyProfiles_TrainingSet.pdf
FreeEnergyProfiles_TrainingSet.pdf
Jan 16, 2022 - Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'
Adobe PDF - 22.6 KB - MD5: 0d5718b3d3b125dbe809175bb9337b6a
Plot of free energy profiles from US simulations for ligand training set complexed with CB8
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