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3.5.1.post4

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acellera-propka

Heuristic pKa calculations with ligands (Acellera fork)

Published30 Jul 2026

Direct dependencies8

Transitive dependenciesNot calculated

README

Version 3.5.1.post4 documentation

PROPKA3

PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure.

For proteins without ligands both versions should produce the same result.

The method is described in the following papers, which you should cite in publications:

Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan H. Jensen. "Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values." Journal of Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan H. Jensen. "PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions." Journal of Chemical Theory and Computation 7, no. 2 (2011): 525-537.

See http://propka.org/ for the PROPKA web server.

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Declared dependencies 12

Native requirements

8 direct targetsNot calculated transitive count

Package / target	Requirement	Relationship
pytest Environment { "extras": "", "marker": "extra == \"test\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`pytest; extra == "test"`	runtime
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sphinx_rtd_theme Environment { "extras": "", "marker": "extra == \"docs\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`sphinx_rtd_theme; extra == "docs"`	runtime
sphinx_sitemap Environment { "extras": "", "marker": "extra == \"docs\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`sphinx_sitemap; extra == "docs"`	runtime
pytest Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`pytest; extra == "dev"`	runtime
numpy Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`numpy; extra == "dev"`	runtime
sphinx Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`sphinx>=3.1; extra == "dev"`	runtime
sphinx_rtd_theme Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`sphinx_rtd_theme; extra == "dev"`	runtime
sphinx_sitemap Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`sphinx_sitemap; extra == "dev"`	runtime
mypy Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`mypy; extra == "dev"`	runtime
coverage Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`coverage; extra == "dev"`	runtime
yapf Environment { "extras": "", "marker": "extra == \"dev\"", "requires_python": ">=3.10", "evaluation": "NOT_EVALUATED" }	`yapf; extra == "dev"`	runtime