Dataset Open Access

Protein language model embeddings and predictions of the human proteome

Christian Dallago; Burkhard Rost

Contact person(s)
Christian Dallago
Supervisor(s)
Burkhard Rost

Residue and sequence embeddings of the human proteome (SwissProt for organism Human, downloaded on 2021.06.09) computed using bio_embeddings (bioembeddings.com) using the ProtT5 embedder at full precision (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3).

Additionally:

- Sequence-level predictions of subcellular localization in 10 classes using LA (https://www.biorxiv.org/content/10.1101/2021.04.25.441334v1)

- Residue-level three state secondary structure prediction (alpha, sheet or other) using models reported in the ProtTrans paper (https://www.biorxiv.org/content/10.1101/2020.07.12.199554v3)

 

Files included:

- human.fasta --> FASTA-formatted sequences of human from SwissProt

- DSSP3_human_ProtT5Sec.fasta --> Secondary structure predictions in three states for each residue of each protein in human.fasta. "H" stands for Helix; "E" stands for Sheet; "C" stands for Other.

- subcell_human_LA_ProtT5.csv --> Subcellular location (10 states) and memrane-boundness (2 states) for each protein in human.fasta

- embeddings_file.h5 --> per-residue embeddings of sequences in human.fasta. Each dataset in the .h5 file represents a protein sequence and contains a matrix of length Lx1024, with L being the length of the protein sequence. Datasets are indexed using integers. The original sequence identifier (from the FASTA header) can be accessed through the "original_id" attribute. See https://docs.bioembeddings.com/v0.2.0/notebooks/open_embedding_file.html for information on how to open the file

- reduced_embeddings_file.h5 --> per-sequence embeddings of sequences in human.fasta (obtained by mean-pooling the residue-embeddings along the length dimension of the protein sequence). Each dataset in the .h5 file represents a protein sequence and contains a vector of size 1024 (meaning, each sequence has the same dimension).

Files (46.7 GB)
Name Size
DSSP3_human_ProtT5Sec.fasta
md5:63eb4cec5465cbfd4cac930fd5db6ee7
13.7 MB Download
embeddings_file.h5
md5:372f4e7b6099288b816ffb73659e469d
46.6 GB Download
human.fasta
md5:313c10a2a28606ad36a85eeb73a5399d
13.6 MB Download
reduced_embeddings_file.h5
md5:e8ae0c5a74bd13ba2e77d1d302dba083
92.0 MB Download
subcell_human_LA_ProtT5.csv
md5:fadaf9b20a0a70b175db77cb084a8b95
1.0 MB Download
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