Tengyu Xie

This study uses molecular dynamics simulations to explore the Na+/H+ antiport mechanism of NhaA, revealing conformational transitions and the role of Lys300 in transport.

AFEXplorer improves protein structure prediction by incorporating user-defined constraints, enhancing the generation of functional conformations.

The paper benchmarks protein structure prediction methods on alternative conformations of membrane proteins, finding biases in deep learning models and showing AlphaFold's energy model is state-neutral.

The paper identifies topological links in AlphaFold-Multimer-predicted protein complexes and proposes a method to detect them, finding about 0.7% of structures contain such links.