PROPKA predicts the pKa values of ionizable groups in proteins based in the 3D structure.
Fortran Perl Python
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Makefile
README.md
dgl.py
pIl.py
propka2.0.pl
propka2.0_2008-11-12.f

README.md

PROPKA 2.0

PROPKA (http://propka.ki.ku.dk/) 16/12/08

Files included: propka2.0_2008-11-12.f, propka2.0.pl, dgl.py and pIl.py.

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

propka2.0.pl:

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

Usage: propka2.0.pl -i xxxx.pdb [-c 'Chain ID(s)' -s -apo -m 'NMR Model Number'] Example: propka2.0.pl -i 1K1I.pdb (chain A w/ ligand FD1)

dgl.py:

Calculates pH dependent free energy using PROPKA output.

Usage: dgl.py xxxx.pdb.pka

pIl.py:

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

Usage: pIl.py xxxx.pdb.pka

Note:

propka2.0.pl can execute PROPKA 2.0 using a previously generated input file with edited ligand pKmodel values (new_xxxx.pdb).

Usage: propka2.0.pl -i new_xxxx.pdb Example: propka2.0.pl -i new_1K1I.pdb (chain A w/ ligand FD1)