Zero-Shot Protein Segmentation (ZPS) Data and Embeddings

uniprotkb_Human.txt

this is a raw text file that contains a downloaded copy of UniProtKB

this inlcudes all reviewed human protein sequences 

we used annotations from this file to copmare to ZPS predictions

uniprotkb_Human_Sequences.fasta

this is a fasta file that contains reviewed human protein sequences

these are the sequences we used as input to ProtT5 to generate protein embeddings

ZPS_Boundaries.tsv

this is a tab separated file that contains the boundaries of protein segments defined by ZPS for reviewed human protein sequences

we used zero-based indexing for the protein boundaries

ZPS_Segment_Embeddings.hdf5

this is a hdf5 file that contains segment embeddings for the human proteome

see "Zero-shot segmentation using embeddings from a language model identifies functional regions in the human proteome" A. G. Sangster 2025 for definition of segment embeddings

segment boundaries in this file are also in zero-based indexing