FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

Anders Steen Christensen; Thomas Wim Hamelryck; Jan Halborg Jensen

doi:10.7717/peerj.277

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

Anders Steen Christensen, Thomas Wim Hamelryck, Jan Halborg Jensen

2 Citationer (Scopus)

75 Downloads (Pure)

Abstract

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

Originalsprog	Engelsk
Artikelnummer	e277
Tidsskrift	PeerJ
Vol/bind	2
ISSN	2167-8359
DOI	https://doi.org/10.7717/peerj.277
Status	Udgivet - 2014

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10.7717/peerj.277Licens: CC BY

2014ChristensenHamelryckJensenPeerJForlagets udgivne version, 1,95 MBLicens: CC BY

Citationsformater

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title = "FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models",

abstract = "We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.",

author = "Christensen, {Anders Steen} and Hamelryck, {Thomas Wim} and Jensen, {Jan Halborg}",

year = "2014",

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AU - Christensen, Anders Steen

AU - Hamelryck, Thomas Wim

AU - Jensen, Jan Halborg

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Y1 - 2014

N2 - We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

AB - We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in a variety of useful formats, such as XYZ or PDB formats, or directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

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JO - PeerJ

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M1 - e277

ER -

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

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