J. M. McBride

The Physical Logic of Protein Machines

This paper explores how the physical principles of protein machines determine their functionality and how sequences encode dynamics and interactions.

AI-predicted protein deformation encodes energy landscape perturbation

The paper uses AlphaFold2 to predict structural deformation from mutations and finds that physical strain correlates well with experimental folding free energy changes, suggesting structures encode energy landscape details.

Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis.

The paper identifies myeloid cell influx and epithelial cell perturbations in ulcerative colitis, linking them to disease severity and anti-TNF therapy non-response.

AlphaFold2 can predict single-mutation effects

The paper evaluates AlphaFold2's ability to predict single-mutation effects using structural and phenotypic correlations across thousands of proteins.

General theory of specific binding: insights from a genetic, mechano-chemical protein model

The paper presents a model combining chemistry, mechanics, and genetics to explain how proteins evolve high specificity through precision and size, making testable predictions about discrimination mechanisms.

Structural asymmetry along protein sequences and co-translational folding

The paper analyzes protein structures to show that structural asymmetry correlates with co-translational folding rates, proposing that evolutionary pressure favors positioning slower-folding elements near the N-terminal.