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

Kamil Tamiola^1,2, Ruud M Scheek², Pieter van der Meulen², Frans A A Mulder^2,3

¹Peptone - The Protein Intelligence Company, Amsterdam, The Netherlands.

²Department of Molecular Dynamics, GBB, University of Groningen, Groningen, The Netherlands.

³Department of Chemistry and Interdisciplinary Nanoscience Center iNANO, Aarhus University, Aarhus, Denmark.

PubMed DOI

Abstract

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 completel…

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