Rachel Kolodny

This study investigates the emergence of two key cofactor-binding protein folds by analyzing their metabolic roles, structural organization, and folding mechanisms.

This paper introduces CLSS, a contrastive learning model that co-embeds protein sequences and structures, revealing evolutionary relationships and structural transitions.

The paper compares structural conservation and divergence across 245 RTK extracellular domains from 54 RTKs, revealing inter-family similarities and unexpected structural differences.

The paper trains AI models to predict codon sequences from amino acid sequences in yeast and bacteria, showing they outperform frequency-based methods and reveal codon usage patterns linked to evolutionary pressures.

This study identifies structural mechanisms explaining how certain RET mutations cause both Hirschsprungs disease and MEN2A by disrupting protein structure and promoting dimerization.

The paper identifies 57 proteins with multiple GPCR domains, analyzes their structures, and suggests new possibilities in GPCR evolution and signal transduction.

The paper investigates the evolutionary origins of β-trefoil proteins by identifying sequence and structural motifs in unrelated lineages, proposing a 'peptide budding' mechanism from an IgG-like β-sandwich.

The paper identifies short protein segments shared between domains thought to have evolved independently, suggesting their role in domain emergence and function.

The paper traces the evolutionary pathway of outer membrane beta barrels, showing how repeat protein topology evolves through strand number changes without domain duplication, driven by membrane environment constraints.