Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

Paul Bauer; Alexandre Barrozo; Miha Purg; Beat Anton Amrein; Mauricio Esguerra; Philippe Barrie Wilson; Dan Thomas Major; Johan Aqvist; Shina Caroline Lynn Kamerlin

doi:10.1016/j.softx.2017.12.001

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

Paul Bauer, Alexandre Barrozo, Miha Purg, Beat Anton Amrein, Mauricio Esguerra, Philippe Barrie Wilson, Dan Thomas Major, Johan Aqvist, Shina Caroline Lynn Kamerlin

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

51 Citationer (Scopus)

Abstract

Atomistic simulations have become one of the main approaches to study the chemistry and dynamics of biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry, with a number of different programs available to perform specialized calculations. We present here Q6, a new version of the Q software package, which is a generalized package for empirical valence bond, linear interaction energy, and other free energy calculations. In addition to general technical improvements, Q6 extends the reach of the EVB implementation to fast approximations of quantum effects, extended solvent descriptions and quick estimation of the contributions of individual residues to changes in the activation free energy of reactions.

Originalsprog	Engelsk
Tidsskrift	SoftwareX
Vol/bind	7
Sider (fra-til)	388-395
Antal sider	8
ISSN	2352-7110
DOI	https://doi.org/10.1016/j.softx.2017.12.001
Status	Udgivet - 2018
Udgivet eksternt	Ja

Adgang til dokumentet

10.1016/j.softx.2017.12.001

Citationsformater

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title = "Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations",

abstract = "Atomistic simulations have become one of the main approaches to study the chemistry and dynamics of biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry, with a number of different programs available to perform specialized calculations. We present here Q6, a new version of the Q software package, which is a generalized package for empirical valence bond, linear interaction energy, and other free energy calculations. In addition to general technical improvements, Q6 extends the reach of the EVB implementation to fast approximations of quantum effects, extended solvent descriptions and quick estimation of the contributions of individual residues to changes in the activation free energy of reactions.",

keywords = "Free energy perturbation, Empirical valence bond, Molecular dynamics simulations, Path integral calculations, PATH-INTEGRAL SIMULATIONS, MOLECULAR-DYNAMICS, COMPUTER-SIMULATION, FORCE-FIELD, ELECTROSTATIC INTERACTIONS, ENZYME CATALYSIS, SAMPLING METHOD, COMBINED QM/MM, ENERGETICS, EVOLUTION",

author = "Paul Bauer and Alexandre Barrozo and Miha Purg and Amrein, {Beat Anton} and Mauricio Esguerra and Wilson, {Philippe Barrie} and Major, {Dan Thomas} and Johan Aqvist and Kamerlin, {Shina Caroline Lynn}",

year = "2018",

doi = "10.1016/j.softx.2017.12.001",

language = "English",

volume = "7",

pages = "388--395",

journal = "SoftwareX",

issn = "2352-7110",

publisher = "Elsevier",

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TY - JOUR

T1 - Q6

T2 - A comprehensive toolkit for empirical valence bond and related free energy calculations

AU - Bauer, Paul

AU - Barrozo, Alexandre

AU - Purg, Miha

AU - Amrein, Beat Anton

AU - Esguerra, Mauricio

AU - Wilson, Philippe Barrie

AU - Major, Dan Thomas

AU - Aqvist, Johan

AU - Kamerlin, Shina Caroline Lynn

PY - 2018

Y1 - 2018

N2 - Atomistic simulations have become one of the main approaches to study the chemistry and dynamics of biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry, with a number of different programs available to perform specialized calculations. We present here Q6, a new version of the Q software package, which is a generalized package for empirical valence bond, linear interaction energy, and other free energy calculations. In addition to general technical improvements, Q6 extends the reach of the EVB implementation to fast approximations of quantum effects, extended solvent descriptions and quick estimation of the contributions of individual residues to changes in the activation free energy of reactions.

AB - Atomistic simulations have become one of the main approaches to study the chemistry and dynamics of biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry, with a number of different programs available to perform specialized calculations. We present here Q6, a new version of the Q software package, which is a generalized package for empirical valence bond, linear interaction energy, and other free energy calculations. In addition to general technical improvements, Q6 extends the reach of the EVB implementation to fast approximations of quantum effects, extended solvent descriptions and quick estimation of the contributions of individual residues to changes in the activation free energy of reactions.

KW - Free energy perturbation

KW - Empirical valence bond

KW - Molecular dynamics simulations

KW - Path integral calculations

KW - PATH-INTEGRAL SIMULATIONS

KW - MOLECULAR-DYNAMICS

KW - COMPUTER-SIMULATION

KW - FORCE-FIELD

KW - ELECTROSTATIC INTERACTIONS

KW - ENZYME CATALYSIS

KW - SAMPLING METHOD

KW - COMBINED QM/MM

KW - ENERGETICS

KW - EVOLUTION

U2 - 10.1016/j.softx.2017.12.001

DO - 10.1016/j.softx.2017.12.001

M3 - Journal article

SN - 2352-7110

VL - 7

SP - 388

EP - 395

JO - SoftwareX

JF - SoftwareX

ER -