qrqxk-PosePredictionProtocol.txt

Name

Convex-PL-rrt

Software

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

System Preparation Parameters

--gen3d for OpenBabel; AllChem.EmbedMolecule(hmol, AllChem.ETKDG()) function from RDkit

System Preparation Method

ligands generation with OpenBabel and RDKit, proteins were taken 'as is'

Pose Prediction Parameters

num_modes = 100, exhaustiveness = 1000 for Autodock Vina; in-house Rapidly-exploring Random Trees sampling.

Pose Prediction Method

docking with Autodock Vina/Convex-PL as a scoring function and rrt sampling method, poses clusterization.

Answer 1

no

Answer 2

no