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

    loading  Checking for direct PDF access through Ovid

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 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

Related Topics

    loading  Loading Related Articles