Fresh RSS blog post! @pilarcossio.bsky.social @emilthomasen.bsky.social and @minhuanli.bsky.social reflect on ensemble measurement and "ensemble resolution" in cryo-EM and X-ray.

Reciprocal Space Station@rs-station.bsky.social · last mo.

1/5 Ensembles are hot in structural biology! But here’s a question we don’t ask enough: What information survives measurement and processing? In our latest blog, @pilarcossio.bsky.social @emilthomasen.bsky.social and @minhuanli.bsky.social have a think 🤔: rs-station.github.io/2026/08/31/a...

OpenBind intends to collect 10,000s of protein-ligand structures & affinities. To prioritize what we collect next, we need cofolding models trained on the latest data. Today we're releasing OpenBind-0 and 717 new ligand-bound structures.

Atomic models powered bioAI's first era. Experiments measure more. @rs-station.bsky.social is joining omsf.io to unlock interpretation of raw exp observables at scale (blog👇); we'll partner with @openfold.io, @openbind.bsky.social , and cryo-EM+X-ray facilities to make this routine. Join us!

Reciprocal Space Station@rs-station.bsky.social · 3mo ago

1/ We're excited to announce that @rs-station.bsky.social is joining the Open Molecular Software Foundation @omsf.io!

What's the future of structural biology look like? Our very own reciprocal astronaut @alisiafadini.bsky.social recently joined Jay Chodaparambil, Melanie Adams-Cioaba, Robin Roehm and @dereklowe.bsky.social for a panel on the future of SBDD in Boston at #IBA2026 to discuss exactly that!

Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇

Yeqing Lin@yeqinglin.bsky.social · 5mo ago

Introducing Genie 3, a generative protein model that substantially advances the state-of-the-art for binder design, increasing in silico success rates by up to 20x on hard multimeric targets. It also debuts a form of inference-time scaling unobserved in other design models. 🧵1/8

#OpenBind announces its first data drop marking a major milestone for AI‑Enabled #DrugDiscovery! It’s the first initiative to generate open, AI‑ready datasets for protein–drug complexes, produced continuously & at industrial scale to enable the next generation of #AI models. https://loom.ly/eIrsqqg

Statistical crystallography as a route to understanding protein dynamics! 1,146 crystal structures of SARS-CoV-2 Mpro reveal correlated motions connecting the dimer interface to the active site. Great to see this work out @tjlane47.bsky.social . Link: rdcu.be/fgzPF

Access alternate functional conformations encoded in AlphaFold’s latent space in a few GPU minutes 👇 We also introduce a novel supervised transfer task: train once on a source (GPCR/kinase/transporter) and apply across the family. Work led by Minji!

Minji Lee@m1nj2.bsky.social · 6mo ago

We introduce ConforNets, a mechanism for conformational control in AlphaFold3 models - SoTA at producing diverse conformations on every multistate benchmark (N=104) - Novel capability: transfer state from one protein to another Outperforms BioEmu, ConforMix and AFsample3 🧵1/8

The more challenging targets CASP gets, the more the structural biology community will learn!

Torsten Schwede@torstenschwede.bsky.social · 6mo ago

The CASP experiment is about to start - and is still short on challenging prediction targets. Ligand complexes, RNA, …

Celebrating #BiophysicsWeek T&C partnered with Phase Space Invaders podcast: Robert Best @sonyahanson.bsky.social @xuhuihuangchem.bsky.social and host @milosz-wieczor.bsky.social Episode 32: Driving the Future of Biophysics: What’s Next in Theory and Computation? www.buzzsprout.com/2313153/epis...

Episode 32 - Robert Best, Sonya Hanson, Xuhui Huang: Driving the Future of Biophysics. What’s Next in Theory and Computation? - Phase Space Invaders (ψ)

With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...

buzzsprout.com

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network

Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...

rdcu.be

#OpenSoftwareAcceleratesScience! 😍

Mohammed AlQuraishi@moalquraishi.bsky.social · 7mo ago

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬 Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes. The Rule of Thumb: If AF3 can’t model it, we want it.

After an Amtrak coding session with @minhuanli.bsky.social, ROCKET team is back at @rs-station.bsky.social HQ! Thank you to Pfizer for welcoming us in Groton and to everyone who attended our seminar online. Exciting work ahead to continue exploring frontiers in structure determination. Back to it 🚀

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

New Title Alert: meteor- a tool for computing crystallographic difference maps that specializes in robust identification of weak signals from minor populations such as bound ligands or time-resolved experimental changes. Learn more here: buff.ly/bgJYF9N #SBGrid #SBGridSoftware #StructuralBiology

GitHub - rs-station/meteor: bringing you the best difference maps

bringing you the best difference maps. Contribute to rs-station/meteor development by creating an account on GitHub.

github.com

Check our new preprint smoothing rugged Cryo-EM landscapes: shorturl.at/gYs9U We tackle practical hurdles of Optimal Transport (OT) loss—differentiability, cost & noise sensitivity—make it a feasible inference workhorse. W/ G. Woollard, D. Herreros, @pilarcossio.bsky.social, K. Dao Duc 🧵👇 (1/9)

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge pubmed.ncbi.nlm.nih.gov/41280101/ #cryoEM

Frontier structural biology chases low occupancies: weak binders in drug discovery & fleeting intermediates in time-resolved studies. When squeezing SNR, confirmation bias looms – you can see what you hope to see in the noise! Enter METEOR ☄️, our denoising+phasing framework! 1/8

Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...

If you missed the live presentation with @alisiafadini.bsky.social and @minhuanli.bsky.social introducing ROCKET, you can watch the video on SBGrid's YouTube channel. More here: buff.ly/nsA12eg #SBGrid #Webinars

ROCKET

SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Belmont University.…

youtu.be

OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

ROCKET's webinar on cryo-EM+crystal data-guided protein structure prediction is now online 🚀: www.youtube.com/watch?v=_29C... Thank you to the many of you who attended and stayed overtime for more Q&A, and especially to @sbgrid.bsky.social for hosting us last week!

ROCKET

YouTube video by SBGrid Consortium

youtube.com

We'll cover our latest work on low resolution applications, a run-through of our codebase, and tutorials of how to run ROCKET on your own data. Join if you're interested!! 🚀

SBGrid Consortium@sbgrid.bsky.social · last yr.

Our monthly software webinars will resume in October with @alisiafadini.bsky.social and @minhuanli.bsky.social covering AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET. Tuesday, October 14, 2025 at 12:00pm ET Register here: buff.ly/uLlQGVr #SBGrid

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.