bio2byte/bio2byte-peptidebuilder

A simple Python library to generate model peptides (incl. capping groups and modified residues)

Bio2byte :: PeptideBuilder

This repository is a fork of PeptideBuilder: A simple Python library to generate model peptides by Matthew Z. Tien, Dariya K. Sydykova, Austin G. Meyer, and Claus O. Wilke.

Installation

You can install bio2byte-peptidebuilder directly from GitHub:

# Create a virtual environment (optional)
python -m venv peptidebuilder
source peptidebuilder/bin/activate

# Install directly from GitHub
pip install git+https://github.com/Bio2Byte/bio2byte-peptidebuilder

Usage

A simple example is shown below. Other examples can be found in the examples/ folder.

# Import the library
from Bio.PDB import PDBIO
import bio2byte.PeptideBuilder as PeptideBuilder
from bio2byte.PeptideBuilder import Geometry

# Dihedral angles for an alpha-helix
helix_phipsi = (-60., -40.)

# Sequence (case insensitive)
sequence = "LYS-GLY-GLU-ARG-GLN-SEP-ALA-VAL-ASP-ILE-ASP".split("-")

# Build an alpha-helical peptide with N-terminal acetyl and
# C-terminal N-methyl capping groups
structure = PeptideBuilder.initialize_ACE()
for res in sequence:
    geo = Geometry.geometry(res)
    geo.phi, geo.psi_im1 = helix_phipsi
    PeptideBuilder.add_residue(structure, geo)
PeptideBuilder.add_terminal_NME(structure)

# Write to PDB file
pdbwriter = PDBIO()
pdbwriter.set_structure(structure)
pdbwriter.save("peptide.pdb")

Added features

Version 1.2.0

• Include new residue geometries
  • SEP (phosphoserine)
  • TPO (phosphothreonine)
  • PTR (phosphotyrosine)
• Include new initialization/termination residues
  • ACE (N-terminal acetyl group)
  • NME (C-terminal N-methyl group)
  • NH2 (C-terminal amide group)
• Allow three-letter residue names in geometry funtion
• Allow alternative residue names for protonation states:
  • ASH (neutral aspartatic acid)
  • GLH (neutral glutamic acis)
  • HIP (protonated histidine)
  • S1P (protonated phosphoserine, net charge = -1)
  • T1P (protonated phosphothreonine, net charge = -1)
  • Y1P (protonated phosphotyrosine, net charge = -1)

Misc

The software is provided to you under the MIT license (see file LICENSE.txt). The most up-to-date version of this software is available at https://github.com/clauswilke/PeptideBuilder.

To test whether your installation works properly, run pytest in the top-level project folder.

Reference

Please cite the original package:

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.