The term “protein universe” refers to the collection of all possible proteins that can be constructed from the small alphabet of 22 proteinogenic amino acids1,2.
In this representation, functionally characterised proteins correspond to stars, protein families to galaxies, and protein superfamilies to clusters of galaxies, surrounded by all those sequences which are evolutionary related but not hitherto functionally characterised or sampled by nature. In this project, we will develop a new web service to navigate through the landscape of this universe that is currently covered by all catalogued natural proteins - the “Protein Universe Atlas”. We will apply deep learning protein language models (pLMs) and abstract protein structure representations to model this landscape in three dimensions (3D), providing users with an interactive and integrative platform that will facilitate the annotation, biocuration and further study of a protein, a set of proteins, or all proteins catalogued so far.