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

Anders S Christensen; Thomas Hamelryck; Jan H Jensen

doi:10.7717/peerj.277

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

PeerJ. 2014 Mar 4:2:e277. doi: 10.7717/peerj.277. eCollection 2014.

Authors

Anders S Christensen¹, Thomas Hamelryck², Jan H Jensen¹

Affiliations

¹ Department of Chemistry, University of Copenhagen , Copenhagen , Denmark.
² Department of Biology, University of Copenhagen , Copenhagen , Denmark.

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.

Keywords: Biochemistry; Computational chemistry; Molecular modeling; Peptides; Proteins.

Grants and funding

Anders S. Christensen is funded by the Novo Nordisk STAR program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.