FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models
- Published
- Accepted
- Subject Areas
- Biochemistry, Computational Biology, Computational Science
- Keywords
- Python, protein, peptides, quantum mechanics, molecular mechanics, computational chemistry, molecular modeling
- Copyright
- © 2013 Christensen et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
- Cite this article
- 2013. FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models. PeerJ PrePrints 1:e169v2 https://doi.org/10.7287/peerj.preprints.169v2
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 XYZ and PDB formats, or optionally 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 Comment
This preprint has been submitted to PeerJ and is currently pending peer-review.