Available databases

We have constructed TM-vec encoded databases on both CATH S100 and Swissprot

The CATH S100 database can be found here and the corresponding metadata can be found here.

These can also be downloaded using wget as follows

wget https://users.flatironinstitute.org/thamamsy/public_www/cath_large.npy
wget https://users.flatironinstitute.org/thamamsy/public_www/cath_large_metadata.npy
wget https://users.flatironinstitute.org/thamamsy/public_www/cath-domain-seqs-large.fa
wget https://users.flatironinstitute.org/thamamsy/public_www/cath-domain-seqs-large.fai

The Swissprot database can be found here and the corresponding metadata can be found here.

These can also be downloaded using wget as follows

wget https://users.flatironinstitute.org/thamamsy/public_www/swiss_large.npy
wget https://users.flatironinstitute.org/thamamsy/public_www/swiss_large_metadata.npy
wget https://users.flatironinstitute.org/thamamsy/public_www/swissprot_seq.fasta
wget https://users.flatironinstitute.org/thamamsy/public_www/swissprot_seq.fai

The TM-vec CATH model can be downloaded as follows

wget https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_cath_model.ckpt
wget https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_cath_model_params.json

See the TM-vec README for a comprehensive list of available models

The DeepBLAST model can be downloaded as follows

wget https://users.flatironinstitute.org/jmorton/public_www/deepblast-public-data/checkpoints/deepblast-pt-l8.ckpt