DL-PeptideBuilder: A simple Python library to generate model (DL-)peptides.

Still working on this:

• add D amino acids support
• add command-line interface support
• add support of more amino acids
• add support of adding amino acids to existing protein
• add energy minimization or conformation optimization support
• further more, add DNA/RNA support

Installation

You can install PeptideConstructor with pip:

pip install PeptideConstructor

PeptideBuilder has two required dependency:

• Biopython for PDB IO.
• Numpy for coordinates calculation.

Usage

After installation, PCcli command could be called in your terminal. PCcli could generage peptide PDB file from sequence in a simple way.

For instance:

PCcli -s AaDdKSQym -o test.pdb

which will generage a test.pdb file in current directory which contains a peptide with sequence of AaDdKSQym, in which, uppercase indicates L amino acids and lowercase indicates D amino acids.

Also, secondary structure and capping of peptide could be applied through PCcli.

Sure you could generage peptide in original way by writing codes. see PeptideBuilder for more infomation.

Post-processing Tools Recommandation:

1. add hydrogens : reduce, TINKER
2. structure optimization: ModRefiner, TINKER/minimize

Others

This repo is based on Lun4m/PeptideBuilder.git and clauswilke/PeptideBuilder.git. Cite their original paper.

Reference: M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder: A simple Python library to generate model peptides. PeerJ 1:e80.