Xiangda Peng

CRANBERRY is a coarse-grained RNA model that includes sugar puckering and noncanonical base pairing, achieving performance comparable to all-atom models in structural predictions and experimental agreement.

This study benchmarks AlphaFold3-like methods for predicting protein-peptide complex structures, showing improved accuracy but challenges in binding site prediction.

This study investigates how temperature affects the fold-switching mechanism of KaiB, a circadian clock protein, showing that proline isomerization is a rate-limiting step.

The paper introduces Z-align, a molecular alignment method that improves binding pose prediction by using topological structural information and flexible optimization of bond lengths and angles.