Darya Stepanenko

Assessing pH-dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 spike glycoprotein

This study investigates whether the FPPR of the SARS-CoV-2 spike glycoprotein undergoes pH-dependent conformational changes, but finds no evidence supporting such a mechanism.

MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction

The paper fine-tunes AlphaFold using high-resolution MHC-peptide crystal structures to improve prediction accuracy for MHC-peptide complex structures, outperforming existing methods in RMSD and lDDT scores.

Phospho-Tune: Enhanced Structural Modeling of Phosphorylated Protein Interactions

This study enhances AlphaFold for predicting phosphopeptide-protein complex structures, achieving higher accuracy in lDDT scores for peptides.

Receptor binding may directly activate the fusion machinery in coronavirus spike glycoproteins

The paper uses all-atom simulations and experimental structures to model how receptor binding activates the fusion machinery in coronavirus spike glycoproteins.