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 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.

ProCS15: A DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

“…The capped AXA tripeptides used to compute the first three terms of Eq 2 were constructed using the FragBuilder Python module (Christensen et al, 2014), which was also used to make different conformations. The acidic and basic amino acids are all modeled in their charged state, including Histidine.…”