A. Bhattarai

Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics

The paper presents cryo-EM structures of the M4 mAChR with ligands and modulators, revealing structural and dynamic insights into allosteric modulation and receptor activation mechanisms.

Mechanism of Tripeptide Trimming by γ-Secretase

This study investigates the mechanism of tripeptide trimming by γ-secretase using biochemical experiments and simulations, revealing structural changes required for the process and how mutations affect it.

Mechanism of ligand recognition by human ACE2 receptor

This study uses LiGaMD simulations to reveal conformational changes in human ACE2 upon ligand binding, suggesting a conformational selection mechanism for ligand recognition.

Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics

This paper introduces LiGaMD, a method to accelerate ligand binding simulations, showing accurate thermodynamics and kinetics compared to experiments.

Mechanisms of γ-Secretase Activation and Substrate Processing

This study uses simulations and experiments to elucidate γ-secretase activation and substrate processing mechanisms, revealing how mutations affect cleavage sites and enzyme function.

Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor

The paper uses ensemble docking with GaMD simulations and Autodock to identify potent allosteric modulators of the A1AR, showing improved performance over rigid docking methods.

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state

This study uses GaMD simulations to show that A1AR activation state affects its interaction with lipid bilayer, revealing coupled dynamics between the receptor and membrane.