Convex-PL-mcmc-rrt-lowerclashes
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, proteins were taken 'as is'
num_modes = 100, exhaustiveness = 1000 for Autodock Vina; Autodock Vina Monte Carlo and in-house Rapidly-exploring Random Trees sampling. Convex-PL was run with a different (lower) penalty function for steric clashes.
docking with Autodock Vina/Convex-PL as a scoring function and two sampling methods, poses clusterization.
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