Releases · gbouras13/phold

You will need to re-install the updated phold database for v0.2.0 using phold install
You will also need to upgrade Foldseek to v9.427df8a

v0.2.0 is a very large update adding:

Improved sensitivity and faster runtime for the foldseek search. This is achieved by clustering the Phold database at --min-seq-id 0.3 -c 0.8 and creating a cluster db before running with foldseek which significantly improves runtime
- Overall, just over 1.1M structures are clustered into around 372k clusters
--cluster-search 1 parameter is added to foldseek search to search against the cluster representatives first and then within each cluster, which increases sensitivity and reduces resource usage compared to phold v0.1.4
Changed default --max_seqs from 1000 to 10000 to improve sensitivity at little resource usage cost
Phold database is expanded adding:
- Extremely conservative high confidence efam proteins with hits to PHROGs.
- 95% dereplicated diversity-generating retroelements (DGRs) from Roux et al.
- 7153 netflax toxin-antitoxin system proteins from Ernits et al.
Adds --ultra_sensitive flag which turns off Foldseek prefiltering for maximum sensitivity. Recommended for small datasets/single phages only.
- This passes the --exhaustive-search parameter to foldseek search
Adds the ability to save ProstT5 embeddings with --save_per_residue_embeddings and --save_per_protein_embeddings
Adds .cif support (e.g. from Alphafold3 server) for structures, not just .pdb file format and changing the CLI to reflect this
Removes some experimental parameters from v0.1.4 (--split etc)

Breaking CLI parameter changes

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