1146-1-rzhhb-PosePredictionProtocol.txt

Name

LigandMatch

Software

LigandMatch 1.0
OpenBabel 2.3.90

System Preparation Parameters

Default 3D pose generation with babel, structure minimization with MMFF94 forcefield and 20000 steps

System Preparation Method

The ligand from PDB 3L5E was extracted from the file and used as a matching template. Contest ligand geometries
were created with OpenBabel from the provided SMILES strings, and structures were minimized with obminimize from the OpenBabel package.

Pose Prediction Parameters

Number of trial poses minimized was 32

Pose Prediction Method

Ligands were aligned with the 3L5E ligand as a template, using a primitive square well potential with an attractive component only, as a rough screen, and then refined minimizing the distance between all atom pairs.

Answer 1

No

Answer 2

Yes