4ery5-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
1000 step minimization (700 receptor fixed, 300 unfixed)

Pose Prediction Method

The most similar ligands from PDB database were chosen, and
target ligands were aligned using LIGSIFT and manual alignment of those, whose alignment was failed by LIGSIFT.
The best poses were subsequently refined using our Monte-Carlo protocol, clusterized, minimized and
rescored both by Vina-like energy function and LIGSIFT. Remark: for molecules starting with DMSO- we
used provided DMSO crystal structure.

Answer 1

No

Answer 2

Yes