Prism Science
@prismscienceorg.bsky.social
Prism is building the full stack of technologies and algorithms necessary to make protein motion measurable, actionable, and predictable. Learn more at prismscience.org
Lattice vibrations contribute to protein-crystal diffuse scattering. Taylor Womack’s new MD analysis tests a step toward separating that signal from internal protein motions. Separation remains a future goal. Read the blog: prismscience.org/research/goo...
Crystal Vibrations in Molecular Dynamics
Dynamic structural data, models, and language to become standard across the field. At scale, this is how we predict conformational ensembles across all of biology.
prismscience.org
How should conformational ensembles be encoded for sharing, visualization, and reuse? Prism is hiring a Senior Scientist, Structural Data Representation to lead schemas, databases, and tool integration. Apply: jobs.ashbyhq.com/astera/2e65a...
Senior Scientist, Structural Data Representation
ABOUT ASTERA: Astera is a private foundation on a mission to steer science and technology toward a better future. We believe the coming years will bring an era of unprecedented scientific and…
jobs.ashbyhq.com
Which features of a conformational ensemble help predict protein function? Prism is hiring a Senior Scientist, Ensemble–Function Mapping to lead work on allostery, catalysis, and binding specificity. Apply: Senior Scientist, Ensemble–Function Mapping jobs.ashbyhq.com/astera/b5272...
Senior Scientist, Ensemble–Function Mapping
ABOUT ASTERA: Astera is a private foundation on a mission to steer science and technology toward a better future. We believe the coming years will bring an era of unprecedented scientific and…
jobs.ashbyhq.com
Sampleworks is now on SBGrid. It combines biomolecular structure predictors with X-ray density maps to guide sampling of protein conformational ensembles. Explore Sampleworks: sbgrid.org/software/tit...
Sampleworks - SBGrid Consortium - Supported Software
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
sbgrid.org
Two teams, two facilities: Mac1 diffuse maps largely agree within measurement error. Study: thestacks.org/publications...
Iterating diffuse scattering protocols in parallel leads to reproducible, high-quality data from Mac1
Two teams measured three-dimensional diffuse scattering maps from SARS-CoV-2 Nsp3 macrodomain (Mac1) crystals to hone protocols and assess reproducibility. The resulting high-quality maps and new…
thestacks.org
AI agents as research papers, and AI’s role in discovery: on the reading list for “Invisible String,” the new podcast from Stephanie Wankowicz and Jaime Fraser. Listen: prismscience.org/research/ttp...
TTPD: Invisible String
Dynamic structural data, models, and language to become standard across the field. At scale, this is how we predict conformational ensembles across all of biology.
prismscience.org
Benchmarking protein predictors? Track preprocessing alongside weights. Feng Yu explains. Read here: prismscience.org/research/cod...
How Silent Code Updates Can Alter Protein Predictions
Dynamic structural data, models, and language to become standard across the field. At scale, this is how we predict conformational ensembles across all of biology.
prismscience.org
We had an incredible few days down in Santa Cruz talking about the amazing science being done within @prismscienceorg.bsky.social!
Protein motion needs a connected stack: measurement, processing, modeling, representations, and interpretation. We’ve set up a Prism space on Hugging Face as a home for future open-source work and scientific resources as they develop. Follow along here: huggingface.co/PrismScience...
PrismScienceOrg (Prism Science)
We are building the foundation to make protein motion measurable, predictable, and actionable.
huggingface.co
Prism’s Research page now has an RSS feed. If RSS is how you keep up with papers, methods, and technical work, you can now add our work on protein motion and conformational ensembles to your reader. prismscience.org/research
Research
Research updates, scholarly work, code and datasets from the Prism team. Filter by topic and by the kind of output you are after.
prismscience.org
Microseeding made a big difference in Katie Lu’s Mac1 crystallization screens: 8 potential hits became 54. She’s using those results to optimize crystals for experiments asking how the crystal environment affects diffuse scattering. prismscience.org/research/kat...
Varying crystallization conditions to study lattice effects on diffuse scattering
Dynamic structural data, models, and language to become standard across the field. At scale, this is how we predict conformational ensembles across all of biology.
prismscience.org
Proteins are always moving. They wiggle. They jiggle. They interact with their surroundings. That movement drives their function. Yet the motion stays mostly invisible. We cannot understand protein function, engineer it, or correct it until we can see the motion and predict it. prismscience.org
Prism | Revealing the Dynamics of Life
Dynamic structural data, models, and language to become standard across the field. At scale, this is how we predict conformational ensembles across all of biology.
prismscience.org
We have not yet tapped the full potential of cryoEM. The method revolutionized structural bio with atomic-level detail, but has largely focused on proteins’ common lowest-energy states. With enough samples, cryoEM sees a broader energy landscape: It can capture *rare* states.
We need new ways to understand disease & design drugs. Protein motion holds the answer.
Diffuse scattering is hard to compare quantitatively across experiments, let alone across synchrotrons. A new DiffUSE Project update shows diffuse maps reproducing across CHESS and ALS. Read the project update: diffuse.science/posts/reprod...
Coffee is for Closers: making Mac1 diffuse scattering reproducible
diffuse scattering reproducible, yay!
diffuse.science
Diffuse scattering can encode correlated protein motions, but standard pipelines often discard it as background. mdx2 is an open-source Python toolkit for carrying that signal through processing. Read @meisborg.bsky.social's overview and try mdx2: diffuse.science/posts/mdx2/
Revealing hidden signals in raw X-ray crystallography data with mdx2
Mdx2 is a powerful and open-source toolkit for diffuse data processing.
diffuse.science
Same mission, but an expanded vision for revolutionizing structural biology to better capture protein motion. Launching September 8.
WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures https://www.biorxiv.org/content/10.64898/2026.08.26.747373v1
DiffUSE is rebuilding GOODVIBES, a forward model for lattice vibrations in diffuse scattering, in fully open-source Python that handles any space group or unit cell. Stephen Thornton posts the progress and open questions. diffuse.science/posts/goodvi... #openscience
Most structures in the PDB report one set of coordinates. The experimental data behind them, in both X-ray crystallography and cryo-EM, is produced by an ensemble. New work recovers that hidden signal at scale in over 60,000 structures. thestacks.org/publications...
Recovering Conformational Heterogeneity from the Protein Data Bank at Scale
An Ensemble Dataset of over 60,000 Structures
thestacks.org
New in BANDICOOT: color each altloc a distinct hue, so you see heterogeneity while you build. Each added alternate conformation is auto hue-shifted from the last; remove them all and the residue returns to bulk color. Configurable and open source! diffuse.science/post/bandico... #compbio
Displaying Conformational Heterogeneity in BANDICOOT
In preparation for hierarchical hetereogeneity encoding, BANDICOOT has a new, more intuitive display mode for alternate conformations.
diffuse.science
An mmCIF file can say a residue has two alternate conformations and how often each appears. It cannot say which alternates occur together in the same copy. A draft proposal for recording that correlation, plus a tool to inspect it: diffuse.science/posts/mmcif-...
mmCIF Explorer and the Heterogeneity Proposal
A playground for the PDBx/mmCIF file exploration, a look at the current proposal for encoding correlated heterogeneity
diffuse.science
In our latest blog, @fraserlab.com graduate student Taylor Womack discusses his roadmap before the results: how he plans to separate lattice vibrations from internal protein motion, which open tools he is using, and which parts are still unresolved. Feedback welcome. diffuse.science/posts/taylor...
Is it all just the lattice?
Towards a complete forward model of diffuse scattering
xtraj.py
New TTPD episode discusses two bioRxiv preprints, revisits the Bethesda Declaration one year on, and public pushback to the OMB funding rule. Plus: where blogs end and peer review begins. diffuse.science/posts/TTPD-16/ #StructuralBiology #Biophysics #OpenScience
Bandicoot reengineers Coot 0.9 for macOS Tahoe: toolbars rebuilt, UI moved from Python 2 to C++, atom picking and labels reworked. Now with built-in pandda.inspect for examining partial-occupancy and alt conformations. diffuse.science/post/bandico...
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.
diffuse.science
Why do protein-function AI models look great on benchmarks but disappoint in practice? Often "leakage": proteins meant for testing slip into training data over time, inflating scores. PLUG is a tool to build cleaner training sets. Read Clay's work: diffuse.science/post/plug-be... #proteinML
Introducing PLUG: A Compiler for Leakage-free Protein Function Benchmarking
Leakage-free Training to Predict Protein Function
diffuse.science
Unlocking protein dynamics requires infrastructure we all can access. ICYMI: all of our software packages live on GitHub, updated in the open: github.com/diff-use
diffUSE
diffUSE has 15 repositories available. Follow their code on GitHub.
github.com
Open science is useful science. One effort we are developing are logbooks where we share research as it happens: what works, what doesn't, what we've learned. Led by DiffUSE Scientist Steve Meisburger (@meisborg.bsky.social). See the latest: diffuse.science/logbook/beam... #OpenScience
