2vinardo-beta
rdkit / MGLTools/ smina (modified)
Assumed pH 4.5 (protonated ASP, GLU )
Tautomers not considered
rdkit used to generate one conformer per ligand using ETKDG method.
prepare_receptor4.py script from MGLTools, which removes water molecules, was used on pdb codes 1MS6, 2FQ9, 2FRQ,
2H7J, 2F1G, 2FRA, 2FUD, 2HH5, 2HXZ, 2OP3, 2R90, 2R9M, 2R9N and 4P6G.
Charged aminoacids and ligands were modified acording to our new parameter scheme in 2vinardo.
Ligands structures were generated with RDKIT from the provided smiles. One conformer was generated per ligand.
Inputs for docking (pdbqt files) were generated with prepare_ligand4.py from MGLTools.
Binding site was kept rigid.
Ligands were docked on all fourteen protein structures, and the pose for which the most negative binding energy was predicted was
used for scoring.
Exhaustiveness=64 #exhaustiveness of global search (default=32)
2Vinardo (beta) scoring function (modification of Vinardo, which is based on Smina, an Autodock Vina fork)
Num_modes=1 #max number of poses to generate
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Ligands were docked on all fourteen protein structures,
and the pose for which the most negative binding energy was predicted was used for scoring.
No
No
2vinardo-beta
rdkit / MGLTools/ smina (modified)
Assumed pH 4.5 (protonated ASP, GLU )
Tautomers not considered
rdkit used to generate one conformers per ligand using ETKDG method.
System Preparation Method: prepare_receptor4.py script from MGLTools, which removes water molecules, was used on pdb code 1MS6, 2FQ9,
2FRQ, 2H7J, 2F1G, 2FRA, 2FUD, 2HH5, 2HXZ, 2OP3, 2R90, 2R9M, 2R9N and 4P6G.
Charged aminoacids and ligands were modified acording to our new parameter scheme in 2vinardo.
Ligands structures were generated with RDKIT from the provided smiles.
Inputs for docking (pdbqt files) were generated with prepare_ligand4.py from MGLTools.
Binding site was kept rigid.
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. We used the crystal structure of fourteen different structures for Cathepsin to perform docking.
The docking run which resulted in the most negative predicted free energy was used for scoring. The scoring function used was
2Vinardo (beta) scoring function (modification of Vinardo, which is based on Smina, an Autodock Vina fork).
No
No