Z. Faidon Brotzakis

Anneal-MaxCal improves kinetic modeling by combining enhanced sampling and maximum-caliber reweighting to estimate accurate transition rates and populations in molecular systems.

This paper proposes a multi-scale model of the pyruvate dehydrogenase complex (PDHc) revealing a nested shell structure that coordinates enzyme communication during pyruvate oxidation.

This study identifies helix III destabilization as the initial trigger for SAA1-76 misfolding by exposing its amyloidogenic core through computational simulations.

The paper develops an in vitro tau aggregation assay combined with machine learning to identify polymorph-specific tau inhibitors, validated in a Drosophila model.

The paper uses a conditional diffusion model to design a small molecule inhibitor of secondary nucleation in alpha-synuclein aggregation, showing it effectively inhibits fibril proliferation.

The paper designs protein sequences with tailored kinetic properties using IF-MD, demonstrating slower unbinding kinetics in nanobody variants against SARS-CoV-2 RBD.

This study uses MEMMI to analyze the transient interactions between the fuzzy coat and cross-β core of Aβ42 filaments, revealing differences in solubility between familial and sporadic AD forms.

This paper introduces Molecular Dynamics Language Models (MDLMs) to generate MD trajectories efficiently, showing they can discover undersampled conformational states in proteins.

This paper introduces AlphaFold-Metainference to predict structural ensembles of disordered proteins using AlphaFold-derived distances in molecular dynamics simulations.

This study presents a method combining deep learning and physics-based models to identify small molecule binders targeting the conformational dynamics of AR-V7, improving hit-rate by 10x.

This paper introduces a single-molecule method using solid-state nanopores and DNA barcoding to detect and characterize misfolded protein oligomers, demonstrating its application to α-synuclein in Parkinson's disease.