Large protein databases reveal structural complementarity and functional locality

Paweł Szczerbiak, Lukasz M. Szydlowski, Witold Wydmański, P. Douglas Renfrew, Julia Koehler Leman and Tomasz Kosciolek ()
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Paweł Szczerbiak: Sano Centre for Computational Medicine
Lukasz M. Szydlowski: Sano Centre for Computational Medicine
Witold Wydmański: Jagiellonian University
P. Douglas Renfrew: Flatiron Institute
Julia Koehler Leman: Open Molecular Software Foundation
Tomasz Kosciolek: Sano Centre for Computational Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Recent breakthroughs in protein structure prediction have led to a surge in high-quality 3D models, highlighting the need for efficient computational solutions. In our work, we examine the structural clusters from the AlphaFold Protein Structure Database (AFDB), a high-quality subset of ESMAtlas, and the Microbiome Immunity Project (MIP). We create a single cohesive low-dimensional representation of the resulting protein space. We show that, while each database occupies distinct regions, they collectively exhibit significant overlap in their functional profiles. High-level biological functions tend to cluster in particular regions, revealing a shared functional landscape despite the diverse sources of data. By creating a representation of protein structure space, localizing functional annotations within this space, and providing an open-access web-server for exploration, this work offers insights for future research concerning protein sequence-structure-function relationships, enabling biological questions to be asked about taxonomic assignments, environmental factors, or functional specificity. This approach is generalizable, thus enabling further discovery beyond findings presented here.

Date: 2025
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DOI: 10.1038/s41467-025-63250-3

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