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PeerJ. 2013 May 21;1:e80. doi: 10.7717/peerj.80. Print 2013.

PeptideBuilder: A simple Python library to generate model peptides.

Author information

1
Department of Biochemistry & Molecular Biology, The University of Chicago , Chicago, IL , USA.

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.

KEYWORDS:

Computational biology; Model peptides; Molecular modeling; Protein structure

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