This colab workspace allows for automatic conservation analysis, in the absence of the updated Weblogo and Consurf servers. Check run all and download the weblogo.png and .txt files to understand the most conserved residues. It then also adds this to the b-factor of an alphafold generated model, to show this in 3D.
It uses this gitlab - https://github.com/WebLogo/weblogo as well as Colabfold servers to generate the a3m files for alignment.
This workbook is based greatly off the Alphafold colab notebook here: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb#scrollTo=G4yBrceuFbf3 and published here:
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: Making protein folding accessible to all. Nature Methods, 2022
The live notebook is available always here: https://colab.research.google.com/drive/1s7N6w2VEjadkJVS9bFzyOLaFZ3uImS0k?usp=sharing, which includes an example output.
To cite this simple notebook use:
Graham C, Stansfeld P and Rodrigues C, Conservation-Colab: Conservation to 3D structure, Github, 2022 , doi: https://zenodo.org/doi/10.5281/zenodo.10062701