jensengroup/propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

What it solves

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes. This is essential for understanding the chemical environment and reactivity of proteins based on their 3D structure.

How it works

It uses an empirical calculation method to predict pKa values, taking into account the 3D structure of the protein or complex. It provides a Python module and a command-line tool (propka3) that can process PDB files to generate these predictions.

Who it’s for

Researchers in biochemistry, structural biology, and computational chemistry who need to determine the pKa values of ionizable groups in protein structures.

Highlights

  • Supports both standalone proteins and protein-ligand complexes.
  • Available as a Python module or a command-line executable.
  • Based on peer-reviewed empirical algorithms for consistent treatment of internal and surface residues.

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