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EvoSite3D

A repository scripts and tutorials around molecular evolution and structural bioinformatics.

Overview

EvoSite3D is designed to identify and analyse functionally significant sites within protein by integrating sequence evolution data with 3D structural information. These tools help researchers understand the relationship between protein evolution, protein function and structural constraints.

Features

  • 3D Structure Analysis: Visualise evolutionary sites in protein 3D structures
  • Sequence Evolution Integration: Combine phylogenetic analysis with structural data
  • Conservation Scoring: Calculate conservation scores for residue positions
  • Structural Context: Analyse evolutionary pressures in different structural environments
  • Visualisation Tools: Generate interactive 3D visualisations of evolutionary hotspots

Installation

For detailed installation instructions, please refer to INSTALL.md.

Tutorials:

Citation

If you use EvoSite3D in your research, please cite:

@software{studer2024evosite3d,
  author = {Romain Studer},
  title = {EvoSite3D: Analysing Evolutionary Sites in 3D Protein Structures},
  year = {2024},
  url = {https://github.com/romainstuder/evosite3d}
}

License

This project is licensed under the MIT License - see the LICENSE file for details.

Author

Romain A. Studer

  • Bioinformatics Data Scientist
  • Previously affiliated with BenevolentAI, EMBL-EBI, UCL, and UNIL.
  • Focus: Protein and nucleotide analysis
  • LinkedIn: romainstuder
  • GitHub: romainstuder

Acknowledgments

  • Thanks to the computational biology community for feedback and testing
  • Built using BioPython, PAML, PyMOL, and other excellent open-source tools

Support

If you encounter any issues or have questions:

  1. Search existing issues
  2. Create a new issue with a minimal reproducible example

This project is under active development. Please report any bugs or feature requests through the GitHub issue tracker.