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