A. Singharoy

Structural mechanism of HP1-dependent transcriptional repression and chromatin compaction

This study determines the cryo-EM structure of HP1 bound to an H2A.Z nucleosome, revealing two binding sites and their roles in transcriptional repression and chromatin compaction.

PDZ Domains from the Junctional Proteins Afadin and ZO-1 Act as Mechanosensors

This study shows that PDZ domains from afadin and ZO-1 act as mechanosensors, forming catch bonds or weakening under mechanical force, affecting cell-cell adhesion stability.

Adaptive Artificial Intelligence to Teach Interactive Molecular Dynamics in the Context of Human-Computer Interaction

This paper uses AI to analyze coordination dynamics in human-AI teams during interactive molecular dynamics tasks to foster discovery curiosity.

Learning Free Energy Pathways through Reinforcement Learning of Adaptive Steered Molecular Dynamics

This paper develops a reinforcement learning framework to compute low free energy pathways between states using adaptive steered molecular dynamics and robotics planning.

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.

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

This paper introduces an adaptive ensemble refinement method for protein structures using MDFF and RADICAL-Cybertools, improving correlation with cryo-EM density maps by 40%.

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.

Characterization and computational simulation of human Syx, a RhoGEF implicated in glioblastoma

This study characterizes human Syx, a RhoGEF involved in glioblastoma, and performs computational simulations to elucidate its structure and allosteric regulation.

Energy Landscape of the SARS-CoV-2 Reveals Extensive Conformational Heterogeneity

The paper uses cryo-EM to analyze the energy landscape of the SARS-CoV-2 spike protein, revealing conformational heterogeneity and dynamic behavior not captured by static models.

Mucin-mimetic glycan arrays integrating machine learning for analyzing receptor pattern recognition by influenza A viruses

This study uses a glycan array platform with machine learning to analyze how influenza A virus binding preferences change with receptor presentation and viral propagation conditions.

Data-guided Multi-Map variables for ensemble refinement of molecular movies

This paper introduces a method to refine molecular simulations using data-guided collective variables, showing improved free-energy estimates and structural accuracy compared to existing models.

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.

Mind reading of the proteins: Deep-learning to forecast molecular dynamics

This paper uses deep learning to predict molecular dynamics from simulation data, finding that non-equilibrium MD is easier to train and performance improves with atom independence assumptions.

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.

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.