3k3fn-LigandScoringProtocol.txt

Name

MC-refine

Software

In house Monte-Carlo/Autodock Vina/RDKIT/LIGSIFT

Parameters

3000 MC steps

Method

Poses were scored by Autodock Vina

Answer 1

No

3k3fn-PosePredictionProtocol.txt

Name

MC-refine

Software

In house/Monte-Carlo/LIGSIFT/RDKIT

System Preparation Parameters

Gasteiger charges

System Preparation Method

Starting ligand conformations were prepared by by RDKIT.

Pose Prediction Parameters

3000 MC steps

Pose Prediction Method

The most similar ligands from PDB database were chosen, and
target ligands were aligned using LIGSIFT. The best poses were subsequently refined using
our Monte-Carlo protocol, clusterized, and rescored both by Vina-like energy function.

Answer 1

No

Answer 2

Yes