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

Bioinformatics. 2018 Jun 15;34(12):2053-2060. doi: 10.1093/bioinformatics/bty033.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Humans
  • Monte Carlo Method
  • Peptides / chemistry*
  • Peptides / metabolism
  • Software*
  • Static Electricity*
  • alpha-Synuclein / chemistry

Substances

  • Peptides
  • alpha-Synuclein