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bioRxiv · 10.1101/2025.10.17.683004

Linking protein residues in literature and structure

Vollmar, M.·Westrip, S.·Nair, S.·Balasubramaniyan, B.·Velankar, S.·Jones, L.·Strickland, P.
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Abstract

Protein structures are crucial in understanding function, mechanism and disease-causing variants of proteins within any living cell. A number of experimental techniques are employed by researchers to determine said structure. Through structure inspection in molecular viewers combined with supporting biochemical and biophysical experiments, scientists are able to identify a proteins function, reaction mechanism and effects caused by sequence variation. These detailed findings supported by experimental results are documented and described in detail in scientific literature and by open sourcing the accompanying data. By writing a detailed report about the findings and providing evidence in additional files and complementary data formats it has become increasingly difficult for a reader, in particular a non-expert, to access the correct additional information and assess the validity of the drawn conclusion based on experimental results. It often requires a reader to resort to a number of different software packages to access the different data types. Here, we present a first-of-its-kind implementation of an artificial intelligence and text mining supported software tool that allows linking of text mentions of specific protein residues to their corresponding counterpart in the respective protein structure. An identified residue is highlighted in the publication text and upon interaction with the annotation, a molecule viewer displays the associated protein structures in the publication which contain said residue. The viewer is complemented by a display table that contains protein structure quality metrics for each occurrence of a residue. As such a reader can now explore a residue of interest they are currently assessing in a publication within its respective protein structure supported by its experimental evidence in a single view and application.

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Vollmar, M., Westrip, S., Nair, S., Balasubramaniyan, B., Velankar, S., Jones, L., Strickland, P.. 2025-10-17. Linking protein residues in literature and structure. https://doi.org/10.1101/2025.10.17.683004

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