https://github.com/bartongroup/sack1g-analysis
This is a GitHub Repository containing the data and code used for an structural analysis of FAM83G and FAM83G-CK1A 3D models
Science Score: 57.0%
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Repository
This is a GitHub Repository containing the data and code used for an structural analysis of FAM83G and FAM83G-CK1A 3D models
Basic Info
- Host: GitHub
- Owner: bartongroup
- Language: Jupyter Notebook
- Default Branch: master
- Size: 122 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Mutations in fragment site of SACK1G abolish interaction with CK1α
This repository includes the code and results of the computational analysis of our pre-print "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish its interaction with the Ser/Thr kinase CK1α", which can be found here.
Directories
Within the AFDB_FAM83B_model and AFDB_FAM83G_model directories, the AlphaFold DB models for human SACK1B (Q5T0W9) and SACK1G (A6ND36) can be found, respectively.
The FAM83B_FRAGSYS directory includes the necessary data from the FRAGSYS [1] analysis of FAM83B/SACK1B, which was employed to hightlight the most likely sites to affect SACK1B function as well as the individual residues within them.
The FAM83G_SS_prediction_JPRED directory include JPred [2] secondary structure predictions for FAM83G/SACK1G employed to complement secondary structure assignments from the AlphaFold [3]three-dimensional structure models.
The FAM83_dimers directory includes the 3D structure models obtained in this work using the Colabfold v1.5.2 [4] implementation of AlphaFold Multimer v3 [5].
Finally, the notebooks directory includes the two Jupyter notebooks employed to carry out the computational analysis described in our manuscript.
Dependencies
References
- Utgés, J.S., MacGowan, S.A., Ives, C.M. et al. Classification of likely functional class for ligand binding sites identified from fragment screening. Commun. Biol. 7, 320 (2024). https://doi.org/10.1038/s42003-024-05970-8
- Alexey Drozdetskiy, Christian Cole, James Procter, Geoffrey J. Barton, JPred4: a protein secondary structure prediction server, Nucleic Acids Res., Volume 43, Issue W1, 1 July 2015, Pages W389–W394, https://doi.org/10.1093/nar/gkv332
- Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). https://doi.org/10.1038/s41586-021-03819-2
- Mirdita, M., Schütze, K., Moriwaki, Y. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022). https://doi.org/10.1038/s41592-022-01488-1
- Abramson, J., Adler, J., Dunger, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024). https://doi.org/10.1038/s41586-024-07487-w
Owner
- Name: Geoff Barton's Computational Biology Group
- Login: bartongroup
- Kind: organization
- Location: Dundee, Scotland, UK
- Website: https://www.compbio.dundee.ac.uk
- Twitter: bartongrp
- Repositories: 57
- Profile: https://github.com/bartongroup