Samuel P. Berry

The paper evaluates how protein fitness models predict and design variants with altered specificity, finding that models biased against such changes can be leveraged by using weighted differences in model scores.

The paper benchmarks sequence- and structure-based protein models using a unified framework, showing structure-based models outperform others in generating functional variants.

The paper investigates the determinants of metal import and specificity in the bacterial transporter DraNramp by analyzing sequence variants and their effects on Mn2+ and Mg2+ import.

This study identifies clade B Nramps as proton-independent transition metal uniporters, suggesting proton coupling evolved later in Nramp evolution.

The paper systematically compares conformational movements in LeuT-fold transporters using distance difference matrices, identifying common and distinct motions across nine proteins.