Create (DL-) peptide PDB files with specified secondary structures
Project description
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:
- add hydrogens : reduce, TINKER
- 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.
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