ftbwp-PosePredictionProtocol.txt

Name

Convex-PL

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, homologous proteins were taken 'as is' from RCSB

Pose Prediction Parameters

num_modes = 100, exhaustiveness = 1000 for Autodock Vina

Pose Prediction Method

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.

Answer 1

yes

Answer 2

yes