M. Shekhar

Human-like dissociations between confidence and accuracy in convolutional neural networks

This study shows that convolutional neural networks exhibit confidence-accuracy dissociations similar to humans when stimulus energy is manipulated, suggesting these effects arise from low-level representation changes rather than cognitive heuristics.

High-resolution structures map the metal import pathway in an Nramp transporter

The paper presents high-resolution structures of the Nramp transporter from Deinococcus radiodurans in different conformations, revealing insights into metal coordination and transport mechanisms.

Revealing a hidden intermediate of rotatory catalysis with X-ray crystallography and Molecular simulations

The paper identifies a hidden intermediate in ATP-hydrolyzing motors using X-ray crystallography and simulations, revealing the rate-limiting step as ADP interaction release.

Protein flexibility and dissociation pathway differentiation can explain onset of resistance mutations in kinases

This paper uses molecular dynamics simulations to explain how a single point mutation in Abl kinase leads to different dissociation pathways and reduced drug residence time for Imatinib.

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

CryoFold determines protein structures from electron density maps using molecular dynamics and physical knowledge, producing ensembles of low-energy conformations validated experimentally.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

The paper evaluates cryo-EM model quality using benchmark maps, showing high accuracy and reproducibility across 13 teams and recommending multiple metrics for model assessment.

Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter

The paper uses HDX-MS, mutagenesis, and MD simulations to show that substrate binding and protonation drive conformational changes in a transporter, while inhibitors prevent this transition.

Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots

The paper introduces a method to analyze conformational changes in biomolecules using single-particle cryo-EM data, revealing functional pathways in RyR1 that differ from discrete structure analyses.

Distinguishing the roles of dorsolateral and anterior PFC in visual metacognition

This study uses TMS to show that DLPFC and aPFC have distinct roles in confidence generation during visual metacognition, with DLPFC lowering confidence and aPFC enhancing it in later task blocks.

Activation and desensitization mechanism of AMPA receptor-TARP complex by cryo-EM

The paper determines the structure of the AMPA receptor-TARP complex using cryo-EM, revealing activation and desensitization mechanisms.