PROPKA predicts the pKa values of ionizable groups in proteins based in the 3D structure.
Fortran Perl Python
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PROPKA ( 16/12/08

Files included: propka2.0_2008-11-12.f,, and

propka2.0_2008-11-12.f: PROPKA 2.0 fortran source code.

Executes PROPKA 2.0 and runs the python scripts and Requires that the PROPKA 2.0 executable file is named 'propka2.0' and located in the pwd or in a bin directory along with and In addition Open Babel is required.

Usage: -i xxxx.pdb [-c 'Chain ID(s)' -s -apo -m 'NMR Model Number'] Example: -i 1K1I.pdb (chain A w/ ligand FD1)

Calculates pH dependent free energy using PROPKA output.

Usage: xxxx.pdb.pka

Calculates the pI (isoelectric point) of the protein using PROPKA output.

Usage: xxxx.pdb.pka

Note: can execute PROPKA 2.0 using a previously generated input file with edited ligand pKmodel values (new_xxxx.pdb).

Usage: -i new_xxxx.pdb Example: -i new_1K1I.pdb (chain A w/ ligand FD1)