Virtual Screening Library Preparation Workflow

Automated workflow for library cleaning and ligand preparations prior to molecular docking.

Breif algorithm introduction:

Library cleaning contains lots of validity check for ligand topology, allowed elements, bond orders, minimum ans maximum number of atoms, radical atoms... etc.

All invalid molecules will be filtered out. All valid molecules would be automactically submitted to batch ligand preparation workflows.

Ligand preparation contains 2D and 3D parts.

2D preparation includes protonation states prediction around pH 7.4, protonation states modification rules, double bond stereo and chiral center isomer enumerations.

3D preparation includes conformation generations and subsequent energy minimizations, filtering, clustering for conformers.

Usage

Users provide molecule library as list of SDF files as inputs. All molecule in the SDF files should contains neccesary information that users want the library saved, such as vendor information, vendor ID, molecule ID, molecule names...etc. All properties listed for each molecules would be saved in the output prepared SDF files after ligand preparations.

For input options please see the job input forms.