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I need to establish protonation of aminoacids composing the studied protein. To my knowledge there are H++ and Pdb2pqr servers that are able to do that. However, they yield quite much different outputs. Do you know about something else I may try to compare with? Maybe there’s something better than these?

Thanks in advance

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  • $\begingroup$ Are you trying to study the protonation state of different aminoacids in a protein? Or you do want to ensure that the protonation states you have are correct? This link has tools to do protonation. $\endgroup$
    – Hemanth Haridas
    Jul 14 at 10:37

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Propka is a standard option used to establish the protonation states of residues in MD. This is a module that can be installed in python. There is thorough documentation online regarding its use. There two main papers that provide a reference to their methods are: https://doi.org/10.1021/ct100578z and https://doi.org/10.1021/ct200133y.

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    $\begingroup$ While this link may answer the question, it is better to include the essential parts of the answer here and provide the link for reference. Link-only answers can become invalid if the linked page changes. - From Review $\endgroup$
    – Vandan Revanur
    Jul 18 at 3:28
  • $\begingroup$ I have added the two main papers that relate to the software, and added some information. The poster requested another method, and I have provided one. $\endgroup$
    – KashmirWalla
    Jul 18 at 3:44
  • $\begingroup$ "Propka is a standard option used to establish the protonation states of residues in MD. This is a module that can be installed in python. There is thorough documentation online regarding its use. There two main papers that provide a reference to their methods are doi.org/10.1021/ct100578z and doi.org/10.1021/ct200133y." 261 characters left. I don't think this answer deserves a downvote (especially now that you made it longer than just 1 line), but it's so short that it fits in the comment box. Please see the highest scoring answers on this site for examples of what's okay. $\endgroup$
    – Nike Dattani
    Jul 18 at 5:58
  • $\begingroup$ I need some 'points' on this site before I can comment. If you can move it to the comment section of their post, that's fine. It's a short question with a short answer. $\endgroup$
    – KashmirWalla
    Jul 18 at 14:47

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