Name

Smina/RF-Score-VS v3

Software

Smina/RF-Score-VS/ODDT/OpenBabel/UCSF Chimera

Parameters

seed 0
exhaustiveness 20
box 20, 20, 20
num_modes=1000
energy_range=1000

Method

Target proteins were selected via blast search in UCSF Chimera.
All protein structures were prepared in UCSF Chimera. Ligand for each structure was retained in separate file.
D3D ligands were docked to all (28) receptors: 3OOF, 3FXV, 3OMM, 3FLI, 3OOK, 3OMK, 3OLF, 3OKI, 3L1B, 3OKH, 3RUU, 3RVF, 3HC6, 3DCU, 3RUT, 3P89, 3HC5, 3DCT, 3P88, 3GD2, 4WVD, 1OSH, 4OIV, 4QE8, 3BEJ, 1OSV, 1OT7, 4QE6.
Docking box was set to 20x20x20 around the crystal ligands.
At most 1000 ligand conformers were retained for further rescoring.
All conformers were rescored with RF-Score-VS v2 and v3.
Each ligand was asigned to a protein based on its similarity to crystal ligands,
and only this receptor was considered for final assesment (called "best receptor").
Top scored poses in RF-Score-VS with Smina score <0 (1 pose for ligand scoring and 5 poses for pose scoring) in best receptor were finally reported.
The RF-Score-VS is sorted by descending order, meaning the greater the value the better the affinity.

Name

Smina/RF-Score-VS v3

Software

Smina/RF-Score-VS/ODDT/OpenBabel/UCSF Chimera

System Preparation Parameters

DockPrep defaults
OpenBabel --gen3d ligands conformations and Gasteiger charges

System Preparation Method

Target proteins were selected via blast search in UCSF Chimera.
All protein structures were prepared in UCSF Chimera. Ligand for each structure was retained in separate file.
D3D ligands were docked to all (28) receptors: 3OOF, 3FXV, 3OMM, 3FLI, 3OOK, 3OMK, 3OLF, 3OKI, 3L1B, 3OKH, 3RUU, 3RVF, 3HC6, 3DCU, 3RUT, 3P89, 3HC5, 3DCT, 3P88, 3GD2, 4WVD, 1OSH, 4OIV, 4QE8, 3BEJ, 1OSV, 1OT7, 4QE6.

Pose Prediction Parameters

Vina scoring funtion (smina implementation)
seed 0
exhaustiveness 20
box 20, 20, 20
num_modes=1000
energy_range=1000

Pose Prediction Method

Docking box was set to 20x20x20 around the crystal ligands.
At most 1000 ligand conformers were retained for further rescoring.
All conformers were rescored with RF-Score-VS v2 and v3.
Each ligand was asigned to a protein based on its similarity to crystal ligands,
and only this receptor was considered for final assesment (called "best receptor").
Top scored poses in RF-Score-VS with Smina score <0 (1 pose for ligand scoring and 5 poses for pose scoring) in best receptor were finally reported.
The RF-Score-VS is sorted by descending order, meaning the greater the value the better the affinity.