Designing proteins requires building a scaffold that positions important functional parts. Current tests only check if the shape appears in a single computer model. But proteins move; stability over time is crucial.
The researchers created a comprehensive of functional motifs and used molecular dynamics simulations to test if statically successful designs stay stable. They evaluated several generative protein-design models.
They found that out of 55 designs that passed the standard test, only 8 remained stable under all dynamic checks. This shows that static evaluation overestimates quality; future design pipelines should include dynamic stability assessment.