Zi Hao Liu

IDPForge: Deep Learning of Proteins with Global and Local Regions of Disorder

IDPForge generates all-atom ensembles of intrinsically disordered proteins and regions using a transformer diffusion model, showing good agreement with experimental data.

Conformational Ensembles of the Disordered 4E-BP2:eIF4E Complex Restrained by smFRET Experiments

The paper generates conformational ensembles of the 4E-BP2:eIF4E complex using smFRET and NMR data, revealing dynamic structural changes and new contact regions.

Competing effects modulate the rate of poly(A) RNA deadenylation in a biomolecular condensate

The paper investigates how competing factors in biomolecular condensates modulate the rate of poly(A) RNA deadenylation by CNOT7, revealing concentration-dependent increases and diffusion-related decreases in enzymatic efficiency.

PRRC2A, PRRC2B and PRRC2C are Stress Granule Proteins that Promote Translation Through Association with the eIF3 complex

This study identifies PRRC2A, PRRC2B, and PRRC2C as stress granule proteins that regulate translation by interacting with the eIF3 complex and 48S PIC factors.

A free energy landscape screen reveals the disordered conformational ensemble of tropoelastin

The paper introduces FELS, a method to screen free energy landscapes for disordered proteins, and applies it to tropoelastin, revealing its conformational ensemble and resolving conflicting models.

Making invisible excited state protein structures visible by combining NMR and machine learning

The paper combines NMR data with AlphaFlow to identify excited state conformers of pro-IL-18, revealing structural insights from transient states.

AlphaFlex: Ensembles of the human proteome representing disordered regions

AlphaFlex generates atomistic conformational ensembles for human proteins with intrinsically disordered regions, integrating AlphaFold models and implicit bilayers for transmembrane proteins.