Protein Structure Landscape

This is a companion repository to the paper:

Szczerbiak P, Szydlowski L, Wydmański W, Renfrew PD, Koehler Leman J, Kosciolek T. Large protein databases reveal structural complementarity and functional locality. bioRxiv, https://doi.org/10.1101/2024.08.14.607935 (2024).

The repository contains data, scripts and notebooks to reproduce main-text Figures and most Supplementary Figures.

Novel methods

The source code for new methods and tools developed during the research is available in dedicated data repositories:

• go2cog
• deepFRI v1.1
• web server

Data sources

We analyzed datasets coming from:

• AFDB: Based on the lists of light and dark proteins stored in https://afdb-cluster.steineggerlab.workers.dev/, we downloaded AlphaFold models using gsutil API directly from the AFDB (see details here: https://github.com/google-deepmind/alphafold/tree/main/afdb) (last access: Feb 14 2024).
• ESMAtlas: We downloaded foldcomp files (regular expression: highquality_clust30.*) directly from https://foldcomp.steineggerlab.workers.dev/ (last access: Jan 23 2024).
• MIP: We downloaded Zenodo archive from https://zenodo.org/records/6611431 (last access: Jan 26 2024).

Web server

The web server is available at: https://protein-structure-landscape.sano.science.

It currently allows for:

• structure search by ID
• structure visualization with PyMOL
• filtering based on:
  • database (AFDB, ESMAtlas, MIP)
  • superCOG functional category
  • protein length
  • pLDDT (for AFDB models only)

The web server will be continuously improved.