Year: 2026
Type: preprint
Abstract: Although use of AI-based tools has gained ground in molecular biology research, their reliability remains a matter of debate. Here, we combined AlphaFold 3 modelling with microscale thermophoresis to investigate the interactions between glucan-binding protein C and the biofilm-inhibiting aptamer and its five derivatives. Structural modelling identified a binding motif on the aptamer and suggested a mechanism of action; however, the predictions were only partially supported by the experimental results. The AlphaFold generated confidence metrics did not correlate directly with the measured binding affinities, indicating that confidence scores can help identify plausible interaction interfaces, but they are not reliable predictors of binding strength. These results highlight the importance of integrating structural prediction with biophysical validation to dissect aptamer–protein recognition. Graphical abstract Graphical abstract presents the workflow of our study from the initial to the further steps. Plus (+) symbolizes the ‘and’ relationship between the prediction and measurement.
Authors: Ákos Harkai, Tamás Mészáros
Institution: Semmelweis University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7221139207