pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides.

Abstract

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. 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. http://protein-nmr.org and https://github.com/PeptoneInc/pepkalc.