A fast approach for structural and evolutionary analysis based on energetic profile protein comparison

Peyman Choopanian, Jaan-Olle Andressoo () and Mehdi Mirzaie ()
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Peyman Choopanian: University of Helsinki
Jaan-Olle Andressoo: University of Helsinki
Mehdi Mirzaie: University of Helsinki

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

Abstract: Abstract In structural bioinformatics, the efficiency of predicting protein similarity, function, and evolutionary relationships is crucial. Our approach proposed herein leverages protein energy profiles derived from a knowledge-based potential, deviating from traditional methods relying on structural alignment or atomic distances. This method assigns unique energy profiles to individual proteins, facilitating rapid comparative analysis for both structural similarities and evolutionary relationships across various hierarchical levels. Our study demonstrates that energy profiles contain substantial information about protein structure at class, fold, superfamily, and family levels. Notably, these profiles accurately distinguish proteins across species, illustrated by the classification of coronavirus spike glycoproteins and bacteriocin proteins. Introducing a separation measure based on energy profile similarity, our method shows significant correlation with a network-based approach, emphasizing the potential of energy profiles as efficient predictors for drug combinations with faster computational requirements. Our key insight is that the sequence-based energy profile strongly correlates with structure-derived energy, enabling rapid and efficient protein comparisons based solely on sequences.

Date: 2025
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DOI: 10.1038/s41467-025-57374-9

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