Research18

The Vision for Prism

Charting the course for dynamic structural biology.

qFitLatent: Learning the Motions of Multiconformers

Learning a latent representation of qFit multiconformers to capture the local dynamics that crystallography usually discards.

WaterFlow: Predicting Ordered Water Molecule Positions on Protein Structures

A flow-matching model for predicting ordered water positions on protein structures, and what it reveals about the limits of the data we train it on.

A Year (plus) of DiffUSE

Science progress over the first year-ish of the DiffUSE Project

Modeling the contribution of harmonic lattice vibrations to the diffuse signal with GOODVIBES

GOODVIBES allows users to model the contribution of harmonic lattice vibrations to diffuse scattering.

Is it all just the lattice?

Taylor's update on his work in the diffUSE project and the roadmap to a complete forward model of diffuse scattering.

Introducing PLUG: A Compiler for Leakage-free Protein Function Benchmarking

Leakage-free Training to Predict Protein Function

Water analysis

Case analysis of consensus water in PDB

Expanding The DiffUSE Project

Expanding The DiffUSE Project

To ensembles and beyond!

Sampleworks is a framework for integrating structural biology observables, structure predictors, and guidance to improve the modeling of conformational ensembles.

In the Cloud

Next steps in diffUSE MD simulations

Quarterly All-Hands Meeting Summary

A report on our October 2025 all-hands meeting

3-2-1 Contact: Comparing MD simulations with diffuse data

Insights from the first comparisons of MD simulations to diffuse data

Optimizing Molecular Dynamics Weights with Machine Learning Tools

Using gradient-based optimization to identify the most physically relevant portions of MD trajectories by maximizing agreement with diffuse scattering data.

From systems operators to systems architects

Opens on seemay.substack.com/p/from-systems-operators-to-systems

Going up a level from data generation to think about the data systems we design and embed

Encoding data for a protein dynamics centered AlphaFold

Re-engineer the encoding and infrastructure of structural biology to embrace dynamics

Modeling Protein Dynamics

Modeling by learning directly from experimental data

Embrace the Mess

A trio of ligand-protein structure papers