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

Kamil Tamiola, Ruud M. Scheek, Pieter van der Meulen, Frans A. A. Mulder

Research output: Contribution to journalArticleAcademicpeer-review

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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.

Original languageEnglish
Pages (from-to)2053-2060
Number of pages8
JournalBioinformatics
Volume34
Issue number12
DOIs
Publication statusPublished - 15-Jun-2018

Keywords

  • INTRINSICALLY DISORDERED PROTEINS
  • GAUSSIAN-CHAIN MODEL
  • CHARGE INTERACTIONS
  • PARKINSONS-DISEASE
  • IONIZABLE GROUPS
  • UNFOLDED STATE
  • PK(A) VALUES
  • TITRATION
  • EQUATIONS
  • ENERGIES

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