CATEGORY
Transform
SOURCE
Durant Lab
DESCRIPTION
Enumerate charge forms using Dimorphite-DL. Typically the number of molecules output is 5 - 10 times greater than the number input.
A typical use is for preparing ligands for docking where having the correct charge state of the ligand can be essential for effective scoring.
INPUTS
A dataset of molecules.
OUTPUTS
A dataset of enumerated charge forms. The UUID of the input molecule is included in the output molecules.
OPTIONS
| Min pH | The minimum pH to consider (default 5.0) |
| Max pH | The maximum pH to consider (default 9.0) |
| Fragment method | The method to use to generate the largest fragment (if multiple fragments are found). Choice is Heavy atom count (HAC) or Molecular weight (MW). |
ADDITIONAL INFO
Dimorphite-DL comes from the Durrant lab at the University of Pittsburgh. For more info see:
Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An open-source program for enumerating the ionization states of drug-like small molecules. J Cheminform 11:14. DOI:10.1186/s13321-019-0336-9
Dimorphite-DL uses the RDKit cheminformatics tookkit.