Z. Smith

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

GrASP identifies druggable protein binding sites using graph neural networks with attention, achieving state-of-the-art performance and high precision.

Glutathione supports lipid abundance in vivo

This study shows that glutathione (GSH) is essential for lipid abundance in adult tissues, particularly in the liver, by repressing NRF2.

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.

Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs

This paper develops a belief propagation method on factor graphs to approximate high-dimensional molecular distribution functions, enabling faster sampling and analysis of conformational dynamics in peptides.

Confronting pitfalls of AI-augmented molecular dynamics using statistical physics

This paper introduces an automated algorithm to improve AI-augmented molecular dynamics by maximizing time-scale separation, tested on three benchmark problems.

Discovering loop conformational flexibility in T4 lysozyme mutants through Artificial Intelligence aided Molecular Dynamics

This study uses AI-aided molecular dynamics to analyze conformational flexibility in T4 lysozyme mutants, revealing how sequence changes affect loop stability and dynamics.

Automatic mutual information noise omission (AMINO): generating order parameters for molecular systems

AMINO generates order parameters for molecular systems using information theory, enabling efficient enhanced sampling and accurate binding affinity calculations.

Can one trust kinetic and thermodynamic observables from biased metadynamics simulations: detailed quantitative benchmarks on millimolar drug fragment dissociation

This study benchmarks infrequent metadynamics against unbiased MD simulations to assess the reliability of kinetic and thermodynamic observables for ligand dissociation from FKBP.

Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization

This paper extends the SGOOP method to construct multi-dimensional reaction coordinates by using conditional probability factorization, demonstrating its effectiveness in simulating complex molecular systems.

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

This study identifies common evolutionary mechanisms that stabilize antibiotic resistance plasmids across different host-plasmid pairs.