Diane L. Lynch

SILCS-Guided Feature Encoding Expands Ligand Recognition at an HBV Core Protein Interface

The paper identifies ligands that bind beyond a known hydrophobic pocket at the HBV core protein interface using molecular dynamics and fragment mapping.

Structural modeling reveals the mechanism of motor ATPase coordination during type IV pilus retraction

The paper models and validates the coordination mechanism between PilT and PilU ATPases during type IV pilus retraction using AlphaFold 3 and molecular dynamics simulations.

Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly

The paper uses Weighted Ensemble simulations to study Hepatitis B virus capsid assembly, revealing new conformations and modulator effects not accessible via standard MD simulations.

Integrative Structure and Function of the Vibrio cholerae Competence Pilus Machine

The paper presents a 3.3 Å cryo-EM map of Vibrio cholerae competence pilus and a full-length pseudoatomic model of the CPM, revealing unique structural features and mechanical properties.

Machine learning of molecular dynamics simulations provides insights into modulation of viral capsid assembly

This paper uses machine learning to classify molecular dynamics simulations of viral capsid assembly intermediates, distinguishing between apo and CAM-bound states with high accuracy.