PeptideBuilder: A simple Python library to generate model peptides
Matthew Z. Tien,
Dariya K. Sydykova,
Austin G. Meyer,
Claus O. Wilke
Affiliations
Matthew Z. Tien
Department of Biochemistry & Molecular Biology, The University of Chicago, Chicago, IL, USA
Dariya K. Sydykova
Section of Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA
Austin G. Meyer
Section of Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA
Claus O. Wilke
Section of Integrative Biology, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA
We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default.
