PypKa Server

Leverage the webserver to quickly start calculating pKa values in your protein of interest



Input Mode


Protein Code

Input File

The input PDB file can be retrieved from the Protein Data Bank, AlphaFold DB or it can be uploaded by the user.

To use a structure from the Protein Data Bank please provide a valid 4-character PBD identification code.

To use a structure from the AlphaFold DB please provide a valid UniProtKB accession number.

To use a uploaded structure please select a PDB file with one of the following naming schemes: AMBER, GROMOS, CHARMM or PDB.


One of the two must be selected

Output PDB

pH value

The available outputs are the pKa values of the titratable amino acids and a PDB formatted file with the most likely protonation state at a given pH value.

Please select the desired output file naming scheme and the target pH value.


We recommend using default parameters. By using them you'll be allowed to query the pKPDB database and retrieve your results instantaneously.

pH min
pH max
pH step

Please set pH min and pH max so that the pKa of all titratable amino acids is withing the titration range. pH step determines the difference between consecutive pH values in the simulated titration.

The default value for the protein dielectric has been found to minimize the error of the prediction. The default value for the solvent dielectric is the experimental value of water at around 273K.

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The PypKa Server is a free resource that is open to all users, including commercial users.