stereochemical-assesments
A repository to perform stereochemical assesments on PDB models generated by X-Ray Diffraction
Science Score: 44.0%
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Low similarity (8.3%) to scientific vocabulary
Repository
A repository to perform stereochemical assesments on PDB models generated by X-Ray Diffraction
Basic Info
- Host: GitHub
- Owner: VedhRKannan
- Language: Python
- Default Branch: main
- Size: 35.6 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Analysis of the secondary structure of the protein
The extract_angles.py script extracts the phi and psi angles, also known as Ramachandran angles, from a Protein Data Bank (PDB) file. It also retrieves the corresponding amino acid residues associated with these torsion angles. The extracted data is then stored in a TSV (Tab-Separated Values) file.
The plot.py script reads the TSV file containing the torsion angles and generates a Ramachandran plot. This plot provides a visual representation of the protein's structural features. By analyzing the alpha helix and beta sheet clusters on the plot, one can assess the quality of the protein model.
This repository offers a convenient tool for rapidly verifying the accuracy of protein models generate through the use of X-Ray Diffraction as well as the AlphaFold AI model by DeepMind, enabling confident utilisation of the model.
Usage
- Run the
extract_angles.pyscript by providing the path to the input PDB file. This will generate a TSV file containing the extracted torsion angles and associated residues. - Execute the
plot.pyscript to create the Ramachandran plot using the generated TSV file: - The resulting plot can be visually examined to evaluate the protein model's quality.
Requirements
- Python 3.x
- Dependencies:
- Biopython
- Numpy
- Matplotlib
- Math
Please ensure that the necessary dependencies are installed before running the scripts.
Owner
- Name: Vedh Kannan
- Login: VedhRKannan
- Kind: user
- Repositories: 1
- Profile: https://github.com/VedhRKannan
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Kannan" given-names: "Vedh" title: "Stereochemical-Assesments" version: 1.0.0 date-released: 2024-02-17 url: "https://github.com/VedhRKannan/Stereochemical-Assesments"
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Dependencies
- Biopython *
- matplotlib *
- numpy *