PeptideConstructor 0.2.1

Create (DL-) peptide PDB files with specified secondary structures

PeptideConstructor: A simple Python library to generate model (DL-) peptides with different secondary structure.

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 easily install PeptideConstructor with pip:

pip install PeptideConstructor

or just clone this repo and run:

python setup.py build
python setup.py install

PeptideConstructor 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.

PCcli -s AaDdKSQym -o test.pdb -ss a -cap 1

parameters :

• -s : peptide sequence. Uppercases indicate L amino acids while lowercases indicate D amino acids
• -o : output PDB file name
• -ss : (optional) secondary structure you want:
  • l for no secondary structure assignment (default)
  • a for alpha helix
  • b for beta sheet
  • la for left hand helix
  • lb for mirror inverted beta sheet
• -cap : (optional) cappings:
  • 0 for no cappings (default)
  • 1 for cappings (ACE in the N terminal and NME in the C terminal)
  • 2 for only adding ACE to the N termial
  • 3 for only adding NME in the C terminal

examples :

Sure you could generage peptide in original way by writing codes.

check examples/ directory for more examples of generating peptide by code.

see PeptideBuilder for more infomation.

Post-processing Tools Recommandation:

1. add hydrogens : reduce, PyMol, TINKER
2. structure optimization: Avogadro/EM, PyMol/sculpt, ModRefiner, TINKER/minimize

Contributing

Pull requests are welcome on GitHub. However, to be accepted, contributions must:

1. Be styled with black
2. Be linted with pylint
3. Be type-checked with mypy
4. Pass the pytest unit tests

Thus, before contributing code make sure the following commands exit without errors when run from the root directory of the PeptideConstructor project:

• pytest
• black .
• mypy PeptideConstructor/
• pylint --rcfile=setup.cfg PeptideConstructor/

Others

This repo is based on Lun4m/PeptideBuilder.git and clauswilke/PeptideBuilder.git.

Cite the original paper:

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.