Kelly M. Thayer

The paper investigates how anticodon nucleotide modifications affect translational tuning via interactions at the ribosomal CAR site.

The paper introduces an analysis pipeline using mdsa-tools to study ribosomal CAR-site dynamics through molecular dynamics simulations and unsupervised learning.

The paper uses molecular dynamics simulations to study the interaction between the ribosome's A site and CAR site, revealing sequence-dependent modulation of hydrogen bonding and π-stacking interactions.

This study quantifies evolutionary changes in p53 sequences across species and assesses p53-protein interactions to explore how p53 regulates longevity and aging mechanisms.

The paper introduces StACKER, a Python tool for analyzing base stacking in nucleic acid structures, and applies it to ribosome simulations to reveal conformational changes linked to translation phenotypes.

The paper shows that adjacent GNN codons slow translation in yeast, likely due to ribosome interactions with the CAR surface during translocation.

The paper investigates GCN codon periodicity in yeast mRNA ramps and shows its impact on translation efficiency through experimental and computational analysis.

The paper identifies universal structural and energetic signatures in prokaryotic promoters that may be recognized by RNA polymerase, despite low sequence conservation.