Ailie Marx

This study analyzes β-turn dynamics using molecular dynamics data to identify six types, including a hybrid I/I' cluster, and shows sequence and structural factors influence their conformational behavior.

The paper shows that synonymous coding affects domain swapping in myoglobin during co-translational folding in E. coli.

The paper reanalyzes data showing codon-dependent differences in backbone conformation in E. coli, using corrected statistical methods and finding consistent small p-values.

This study uses density-guided AlphaFold3 to reveal unmodeled conformational heterogeneity in β2-microglobulin from crystallographic maps.

This paper shows how AlphaFold3 can be guided by experimental data to predict accurate protein ensembles, including alternate conformations.

The paper shows that adding peptide tags to scaffold proteins reduces prediction accuracy in chimeric proteins, but appending their multiple sequence alignment restores accuracy.

The paper uses molecular dynamics simulations to show that proteins can adopt dual, transiently stable conformations, which current prediction methods fail to capture.

The paper analyzes protein structures to show that amino acid pairs have conformational preferences and that mutations' effects on protein stability depend on their adjacent amino acid context.