Proteins in motion.

Molecular simulation and AI forprotein science and therapeutic discovery.

Our research Publications

Rhodopsin (wild type), 1 µs molecular dynamics simulation

Molecular modeling & protein dynamics

How proteins move, interact, and respond to changes in sequence and environment.

Rhodopsin with the residues lining the retinal pocket in gold

AI for protein function

Models that connect sequence and structure to measurable biological properties.

The drug abiraterone (gold) bound above the heme inside CYP17A1 (PDB 3RUK)

Computational therapeutic design

Proteins, peptides, antibodies, and small molecules for therapeutic discovery.

RSV fusion protein bound by antibody motavizumab, predicted escape sites in gold (PDB 4ZYP)

Evolution & therapeutic resistance

How mutations reshape stability, binding, and viral escape.

Current focus

How does sequence tune the way an opsin senses light?

Small changes in an opsin's amino-acid sequence shift the wavelength it responds to. We combine atomistic simulation with machine learning to predict that shift.

Retinal, the light-sensing pigment, held in its pocket inside rhodopsin, from our own simulation.

Selected publications

All publications

Deep-sea fish reveal an alternative developmental trajectory for vertebrate vision

LG Fogg, S Isari, JE Barnes, JS Patel, NJ Marshall, W Salzburger, et al.

Science Advances 12(7):eadx2596, 2026

Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data

LA Chi, JE Barnes, JS Patel, FM Ytreberg

Scientific Reports 14(1):23122, 2024

Vision using multiple distinct rod opsins in deep-sea fishes

Z Musilova, F Cortesi, M Matschiner, WIL Davies, JS Patel, SM Stieb, et al.

Science 364(6440):588–592, 2019

Interested in proteins, computation, or both?

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