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Updated: Feb 15, 2026

Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins
Published on: January 6, 2017
pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides
Kamil Tamiola1,2, Ruud M Scheek2, Pieter van der Meulen2
1Peptone - The Protein Intelligence Company, Amsterdam, The Netherlands.
Motivation:
Polypeptide sequence length is the single dominant factor hampering the effectiveness of currently available software tools for de novo calculation of amino acid-specific protonation constants in disordered polypeptides.
Results:
We have developed pepKalc, a robust simulation software for the comprehensive evaluation of protein electrostatics in unfolded states. Our software completely removes the limitations of the previously reported Monte-Carlo approaches in the computation of protein electrostatics by using a hybrid approach that effectively combines exact and mean-field calculations to rapidly obtain accurate results. Paired with a modern architecture GPU, pepKalc is capable of evaluating protonation behavior for an arbitrary-size polypeptide in a sub-second time regime.
Availability And Implementation:
http://protein-nmr.org and https://github.com/PeptoneInc/pepkalc.
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