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Progres release notes

v1.1.0 - Jan 2026

  • The Big Fantastic Virus Database (BFVD) is made available to search against.
  • The embedding mode for generating databases to search against can now split structures into domains with Chainsaw.

v1.0.0 - Apr 2025

Stable version of Progres to accompany the published paper (https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf042/8107707).

  • A bug in loading the trained model when the data has not been downloaded is fixed.

v0.2.7 - Sep 2024

  • Bugs in domain splitting with a blank chain ID and Mac multithreading are fixed.

v0.2.6 - Aug 2024

  • Python packaging issues are fixed.

v0.2.5 - Aug 2024

  • Structures can now be split into domains with Chainsaw before searching, with each domain searched separately. This makes Progres suitable for use with multi-domain structures.
  • The whole PDB split into domains with Chainsaw is made available to search against.
  • Hetero atoms are now ignored during file reading.
  • Example files are added for searching and database embedding.

v0.2.4 - Jul 2024

  • The score mode is added to calculate the Progres score between two structures.

v0.2.3 - May 2024

  • Incomplete downloads are handled during setup.

v0.2.2 - Apr 2024

  • The environmental variable PROGRES_DATA_DIR can be used to change where the downloaded data is stored.
  • A Docker file is added.
  • Searching on GPU is made more memory efficient.
  • Bugs when running on Windows are fixed.

v0.2.1 - Apr 2024

  • The AlphaFold database TED domains are made available to search against, with FAISS used for fast searching.
  • Pre-embedded databases are stored as Float16 to reduce disk usage.
  • Datasets and scripts for benchmarking (including for other methods), FAISS index generation and training are made available.

v0.2.0 - Mar 2023

  • Change model architecture to use 6 EGNN layers and tau torsion angles, making it faster and SE(3)-invariant rather than E(3)-invariant.
  • The AlphaFold models for 21 model organisms are made available to search against.
  • The trained model and pre-embedded databases are downloaded from Zenodo rather than GitHub when first running the software.

v0.1.3 - Nov 2022

  • Fix data download.

v0.1.2 - Nov 2022

  • Add ECOD database.
  • Use versioned model directory.

v0.1.1 - Nov 2022

  • Add einops dependency.
  • Add code for ECOD database.

v0.1.0 - Nov 2022

Initial release of the progres Python package for fast protein structure searching using structure graph embeddings.