Jonathan Martin

This paper introduces a structure-aware generative framework that integrates geometric encoding and coevolutionary constraints to map, cluster, and design protein sequences, improving homology detection and structure-guided sequence generation.

The paper identifies and characterizes nitrate-binding affinity differences in staphylococcal NreA homologues, showing that a conserved binding pocket allows recognition while distal sequence variation tunes affinity.

This study identifies DrmA, a DUF998 family protein, as a regulator of cationic glycolipid levels and a contributor to high-level daptomycin resistance in E. faecalis.

This study uses deep learning and coevolutionary analysis to explore how sequence variation and structural dynamics influence thermal adaptation in cytosolic malate dehydrogenase.