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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

FragBuilder : an efficient Python library to setup quantum chemistry calculations on peptides models. / Christensen, Anders Steen; Hamelryck, Thomas Wim; Jensen, Jan Halborg.

In: PeerJ, Vol. 2, e277, 2014.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Christensen, AS, Hamelryck, TW & Jensen, JH 2014, 'FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models', PeerJ, vol. 2, e277. https://doi.org/10.7717/peerj.277

APA

Christensen, A. S., Hamelryck, T. W., & Jensen, J. H. (2014). FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models. PeerJ, 2, [e277]. https://doi.org/10.7717/peerj.277

Vancouver

Christensen AS, Hamelryck TW, Jensen JH. FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models. PeerJ. 2014;2. e277. https://doi.org/10.7717/peerj.277

Author

Christensen, Anders Steen ; Hamelryck, Thomas Wim ; Jensen, Jan Halborg. / FragBuilder : an efficient Python library to setup quantum chemistry calculations on peptides models. In: PeerJ. 2014 ; Vol. 2.

Bibtex

@article{1ce21317c94a40beaee3e4001b87204d,
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",
doi = "10.7717/peerj.277",
language = "English",
volume = "2",
journal = "PeerJ",
issn = "2167-8359",
publisher = "PeerJ",

}

RIS

TY - JOUR

T1 - FragBuilder

T2 - an efficient Python library to setup quantum chemistry calculations on peptides models

AU - Christensen, Anders Steen

AU - Hamelryck, Thomas Wim

AU - Jensen, Jan Halborg

PY - 2014

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.

U2 - 10.7717/peerj.277

DO - 10.7717/peerj.277

M3 - Journal article

C2 - 24688855

VL - 2

JO - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - e277

ER -

ID: 131121723