Name		Name	Last commit message	Last commit date
parent directory ..
data		data
inverse_folding		inverse_folding
lm-design		lm-design
protein-programming-language		protein-programming-language
variant-prediction		variant-prediction
README.md		README.md
contact_prediction.ipynb		contact_prediction.ipynb
esm2_infer_fairscale_fsdp_cpu_offloading.py		esm2_infer_fairscale_fsdp_cpu_offloading.py
esm_structural_dataset.ipynb		esm_structural_dataset.ipynb
sup_variant_prediction.ipynb		sup_variant_prediction.ipynb

README.md

What's in this directory

The notebooks are introduced and summarized in ../README.md
data/some_proteins.fasta and its smaller version, data/few_proteins.fasta are a random selection of UniRef50 sequences used in the second example of ../README.md
data/1a3a_1_A.a3m, data/1xcr_1_A.a3m, data/5ahw_1_A.a3m are MSAs distributed with trRosetta, used in contact_prediction.ipynb
data/P62593.fasta is introduced and used in sup_variant_prediction.ipynb
Example MSAs genereated in the same way as the MSAs used for MSA Transformer pre-training:
- data/UniRef50_E9K9Y4.a3m, data/UniRef50_UPI0003108055.a3m, data/UniRef50_UPI0003674933.a3m, from the same sequences as trRosetta: data/hhblits_uniclust_2017_10_1a3a_1_A.a3m, data/hhblits_uniclust_2017_10_1xcr_1_A.a3m, data/hhblits_uniclust_2017_10_5ahw_1_A.a3m.
- Generated with: hhblits -i UniRef50_$id.fas -oa3m UniRef50_$id.a3m -n 3 -d /uniclust30_2017_10/uniclust30_2017_10.
esm2_infer_fairscale_fsdp_cpu_offloading.py shows how to load the ESM-2 15B model with Fairscale's FSDP's CPU offloading capability on a single GPU