Enumerate charges

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 pHThe minimum pH to consider (default 5.0)
Max pHThe maximum pH to consider (default 9.0)
Fragment methodThe 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.