├── .gitignore ├── PCA_on_MSA.ipynb ├── README.md ├── WHY_MDS_WORKS.ipynb ├── af3_hypothesis.ipynb ├── categorical_jacobian ├── 2onk_analysis.ipynb ├── README.md ├── esm2.ipynb ├── esm3.ipynb ├── evo_trna_example.ipynb ├── gLM2.ipynb ├── proteinmpnn.ipynb └── utils.py ├── categorical_jacobian_esm2.ipynb ├── floyd_mds.ipynb ├── invcov_floyd_mds.ipynb ├── notebooks ├── get_sse.ipynb ├── miniaturize_using_esm3.ipynb ├── replacement_scan.ipynb └── upgma_nj.ipynb ├── rmsd_compute.ipynb ├── temp ├── fig2a.ipynb └── msa.a3m └── test └── floyd_offset.ipynb /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /PCA_on_MSA.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sokrypton/ColabBio/HEAD/PCA_on_MSA.ipynb 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