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PeptideBuilder: A simple Python library to generate model peptides

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Author(s): Matthew Z. Tien | Dariya K. Sydykova | Austin G. Meyer | Claus O. Wilke

Journal: PeerJ
ISSN 2167-8359

Volume: 1;
Start page: e80;
Date: 2013;
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Keywords: Protein structure | Molecular modeling | Computational biology | Model peptides

ABSTRACT
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.
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