propka3.4 predicts pKa of CYS as 99.99 every time.

jensengroup / propka

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

http://propka.org

GNU Lesser General Public License v2.1

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propka3.4 predicts pKa of CYS as 99.99 every time. #122

Closed danny305 closed 3 years ago

danny305 commented 3 years ago

I ran propka3.4 on the pdb files 6ij6, 6ilw, and 6ky5 and it consistently predicts the pKa of all CYS residues to be 99.99. I am assuming this is a bug. Its my first time using the software tool.

sobolevnrm commented 3 years ago

Do these CYS residues participate in disulfide bridges?

danny305 commented 3 years ago

Yeah all 4 of them do.

sobolevnrm commented 3 years ago

In that case, the 99.99 is the intended behavior. The code is not able to model coupled redox/titration reactions. Please let us know if you have any additional questions. Thanks.