Research43

The Tortured Proteins Department: Introducing Prism

Podcast introducing Prism

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

Coffee is for Closers: making Mac1 diffuse scattering reproducible

diffuse scattering reproducible, yay!

The Tortured Proteins Department, Episode 17

The Tortured Proteins Department Podcast, Episode 17

Revealing hidden signals in raw X-ray crystallography data with mdx2

Mdx2 is a powerful and open-source toolkit for diffuse data processing.

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.

Displaying Conformational Heterogeneity in BANDICOOT

In preparation for hierarchical hetereogeneity encoding, BANDICOOT has a new, more intuitive display mode for alternate conformations.

mmCIF Explorer and the Heterogeneity Proposal

A playground for the PDBx/mmCIF file exploration, a look at the current proposal for encoding correlated heterogeneity

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.

Cruel Kinase Summer, Episode 16

The Tortured Proteins Department Podcast, Cruel Kinase Summer

BANDICOOT: Coot 0.9 That Runs on MacOS Tahoe

Reviving Coot 0.9 for MacOS Tahoe as Bandicoot, a bespoke and integrated molecular modeling environment.

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

Leakage-free Training to Predict Protein Function

The Tortured Proteins Department, Episode 15

The Tortured Proteins Department Podcast, Episode 15

DiffUSE Open Science Policies and Guidelines

Astera’s open science policy is that all work products created with Astera dollars must be made available under CC-BY (attribution required, recommended) or CC 0 (completely free use). Even if it’s…

Open Development for Biomolecular Ensemble Generation

The diffUSE Project releases *sampleworks*, moving beyond open science to science in the open

The Tortured Proteins Department, Episode 14

The Tortured Proteins Department Podcast, Episode 14

Encoding Heterogeneity in mmCIF Files

Explicitly encoding hierarchical heterogeneity in mmCIF files

Water analysis

Case analysis of consensus water in PDB

The Tortured Proteins Department, Episode 13

The Tortured Proteins Department Podcast, Episode 13

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.

Shake It Up!

MD simulations of changes in diffuse scattering depending on ligand binding

DiffUSE January 2026 Retreat: From Coast to Coast, Diffuse Scattering Reproduces

A report on our January 2026 all-hands meeting

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

Ensemble <-> Multiconformer Model Conversion

Converting between ensemble and multiconformer models

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.

Taylor's Diffuse Rotation

What Taylor got done during his rotation.

Sample Shipping

Sample preparation for future beamtimes

The Barrier of Barrier Materials

It is hard to have happy crystals and low background at the same time

Next Steps with the Macrodomain Data

What to do next about improving macrodomain data quality and processing

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

Join diffUSE!

Open Jobs at diffUSE

Let's dance!

Molecular-dynamics simulations of diffuse scattering

Getting our feet wet

Data collection at ALS beamline 8.3.1 on June 24, 2025

The DaVinci Dude Dance

Calculated diffraction patterns from different models

Embrace the Mess

A trio of ligand-protein structure papers