Convex-PL
OpenBabel 2.3.2, RDKit 2017.03.3 for 3D coordinates generation; Autodock Vina and Convex-PL for pose prediction, Knodle for parametrization of small molecules
num_modes = 100, exhaustiveness = 1000 for Autodock Vina
Convex-PL
OpenBabel 2.3.2, RDKit 2017.03.3 for 3D coordinates generation; Autodock Vina and Convex-PL for pose prediction, Knodle for parametrization of small molecules
--gen3d for OpenBabel; AllChem.EmbedMolecule(hmol, AllChem.ETKDG()) function from RDkit
ligands generation with OpenBabel and RDKit, homologous proteins were taken 'as is' from RCSB
num_modes = 100, exhaustiveness = 1000 for Autodock Vina
docking with Autodock Vina/Convex-PL as a scoring function, poses clusterization. Some of the poses were then rejected or chosen with help of visual inspection.
yes