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.

The paper uses sequence data and machine learning to identify novel substrates and lipid products of MprF in bacteria.