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

doi:10.1093/bioinformatics/bty033

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

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

10 Citations (Scopus)

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 language	English
Journal	Bioinformatics
Volume	34
Issue	12
Pages (from-to)	2053-2060
Number of pages	8
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/bty033
Publication status	Published - 15 Jun 2018

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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.",

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PepKalc: Scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides. / Tamiola, Kamil; Scheek, Ruud M.; Van Der Meulen, Pieter et al.
In: Bioinformatics, Vol. 34, No. 12, 15.06.2018, p. 2053-2060.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

TY - JOUR

T1 - PepKalc

T2 - Scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides

AU - Tamiola, Kamil

AU - Scheek, Ruud M.

AU - Van Der Meulen, Pieter

AU - Mulder, Frans A.A.

PY - 2018/6/15

Y1 - 2018/6/15

N2 - 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.

AB - 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.

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JO - Bioinformatics

JF - Bioinformatics

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PepKalc: Scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides

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