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

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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 language	English
Pages (from-to)	2053-2060
Number of pages	8
Journal	Bioinformatics
Volume	34
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/bty033
Publication status	Published - 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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pepKalcFinal publisher's version, 302 KBLicence: Taverne

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title = "pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides",

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.",

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

author = "Kamil Tamiola and Scheek, {Ruud M.} and {van der Meulen}, Pieter and Mulder, {Frans A. A.}",

year = "2018",

month = jun,

day = "15",

doi = "10.1093/bioinformatics/bty033",

language = "English",

volume = "34",

pages = "2053--2060",

journal = "Bioinformatics",

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publisher = "Oxford University Press",

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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.

KW - INTRINSICALLY DISORDERED PROTEINS

KW - GAUSSIAN-CHAIN MODEL

KW - CHARGE INTERACTIONS

KW - PARKINSONS-DISEASE

KW - IONIZABLE GROUPS

KW - UNFOLDED STATE

KW - PK(A) VALUES

KW - TITRATION

KW - EQUATIONS

KW - ENERGIES

U2 - 10.1093/bioinformatics/bty033

DO - 10.1093/bioinformatics/bty033

M3 - Article

SN - 1367-4803

VL - 34

SP - 2053

EP - 2060

JO - Bioinformatics

JF - Bioinformatics

IS - 12

ER -

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

Abstract

Keywords

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