OpenBabel --gen3d ligands conformations and Gasteiger charges
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.
Vina scoring funtion (smina implementation)
box 20, 20, 20
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.