Research
- Data Collection
- and Modeling, General, Biology, and Encoding
The Vision for Prism
Charting the course for dynamic structural biology.
- Blog
- Modeling
qFitLatent: Learning the Motions of Multiconformers
Learning a latent representation of qFit multiconformers to capture the local dynamics that crystallography usually discards.
- Blog
- Modeling
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.
- Blog
- Data Collection
- and Modeling, Biology, and Infrastructure
A Year (plus) of DiffUSE
Science progress over the first year-ish of the DiffUSE Project
- Blog
- Modeling
WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures
Opens on biorxiv.org/content/10.64898/2026.08.26.747373v1
A flow-matching generator and confidence model for predicting the positions of ordered water molecules in protein structures. WaterFlow outperforms the existing state of the art at every precision level, and its novel predictions often fall on positive difference density, placing waters at sites the original depositions omitted. Preprint, bioRxiv. DOI: 10.64898/2026.08.26.747373
- Scholarly Work
- Modeling
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.
- Blog
- Modeling
Recovering Conformational Heterogeneity from the Protein Data Bank at Scale
Opens on thestacks.org/publications/qfit-at-scale
An ensemble dataset of over 60,000 structures. Applying qFit to re-refined PDB entries better than 2 Å to recover latent conformational heterogeneity at scale — the largest dataset of experimentally derived ensemble models. DOI: 10.82153/pff0-ck46
- Scholarly Work
- Modeling
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.
- Blog
- Modeling
Introducing PLUG: A Compiler for Leakage-free Protein Function Benchmarking
Leakage-free Training to Predict Protein Function
- Blog
- Modeling
macromolecular-observables
Opens on github.com/prism-science/macromolecular-observables
A package for conveying and transforming information about proteins — ensembles, structures, and measurements. A joint project of Radial Science and Reciprocal Spaceship.
- Code
- Modeling
Supplying a user-defined bulk solvent map for refinement
Opens on thestacks.org/publications/method-bulksolvent
A patch to Phenix refinement that lets users supply their own bulk solvent map in place of the default flat binary mask, opening refinement to MD, 3D-RISM and neural-network solvent models. DOI: 10.82153/2me0-hd96
- Scholarly Work
- Modeling
sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation
Opens on thestacks.org/publications/sampleworks-release
A modular framework for generating and evaluating biomolecular conformational ensembles from structure predictors guided by experimental data, benchmarked across Boltz-2, Protenix and RosettaFold3. DOI: 10.82153/jkxj-tw08
- Scholarly Work
- Modeling
consensus_water_analysis
Opens on github.com/prism-science/consensus_water_analysis
Analysis of consensus ordered water across Protein Data Bank depositions.
- Code
- Modeling
qFitLatent
Opens on github.com/prism-science/qFitLatent
A model to learn qFit multiconformer dynamics with an invariant backbone.
- Code
- Encoding
- and Modeling
mmcif_encoding
Opens on github.com/prism-science/mmcif_encoding
Examples and descriptions related to mmCIF encoding of hierarchical heterogeneity.
- Code
- Modeling
Water analysis
Case analysis of consensus water in PDB
- Blog
- Modeling
md-workflows
Opens on github.com/prism-science/md-workflows
Molecular dynamics workflows for simulating diffuse scattering.
- Code
- Diffuse Scattering
- and Modeling
goodvibes
Opens on github.com/prism-science/goodvibes
Lattice vibration model for diffuse scattering
- Code
- Data Collection
- and Modeling, Biology, and Infrastructure
Expanding The DiffUSE Project
Expanding The DiffUSE Project
- Blog
- Modeling
To ensembles and beyond!
Sampleworks is a framework for integrating structural biology observables, structure predictors, and guidance to improve the modeling of conformational ensembles.
- Blog
- Modeling
WaterFlow
Opens on github.com/prism-science/WaterFlow
Predicting water molecule placements on protein surfaces using flow matching conditioned on learned protein structure embeddings.
- Code
- Modeling
- and Data Collection
In the Cloud
Next steps in diffUSE MD simulations
- Blog
- Data Collection
- and Modeling, Biology, and Infrastructure
Quarterly All-Hands Meeting Summary
A report on our October 2025 all-hands meeting
- Blog
- Modeling
- and Data Collection
3-2-1 Contact: Comparing MD simulations with diffuse data
Insights from the first comparisons of MD simulations to diffuse data
- Blog
- Modeling
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.
- Blog
- Modeling
sampleworks
Opens on github.com/prism-science/sampleworks
Framework for modified sampling from biomolecular generative models
- Code
- Data Collection
- and Modeling, Biology, and Infrastructure
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
- Blog
- Encoding
- and Modeling
Encoding data for a protein dynamics centered AlphaFold
Re-engineer the encoding and infrastructure of structural biology to embrace dynamics
- Blog
- Modeling
Modeling Protein Dynamics
Modeling by learning directly from experimental data
- Blog
- Modeling
Embrace the Mess
A trio of ligand-protein structure papers
- Blog