iiinova — where your digital self keeps evolving

Alisia Fadini @alisiafadini.bsky.social · 04/09/2026

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.

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Etowah Adams @etowah0.bsky.social · 21/08/2026

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.

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Alisia Fadini @alisiafadini.bsky.social · 21/07/2026

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!

omsf.io

Open Molecular Software Foundation

Making bonds Building open source software and communities for the molecular sciences.

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Reciprocal Space Station @rs-station.bsky.social · 13/05/2026

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!

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Mohammed AlQuraishi @moalquraishi.bsky.social · 08/05/2026

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👇

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OpenBind @openbind.bsky.social · 06/05/2026

#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. loom.ly/eIrsqqg

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Alisia Fadini @alisiafadini.bsky.social · 02/05/2026

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

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Alisia Fadini @alisiafadini.bsky.social · 21/04/2026

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!

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 21/04/2026

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

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Alisia Fadini @alisiafadini.bsky.social · 01/04/2026

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

rdcu.be

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...

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Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026

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

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Torsten Schwede @torstenschwede.bsky.social · 13/03/2026

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.

The Critical Assessment of Structure Prediction (CASP) experiment is calling for prediction targets: Immune Complexes, Organic Ligand-Protein Complexes, Nucleic Acids and Complexes, Conformational Ensembles, Difficult Protein Structures and Complexes.
Rule of Thumb: If AlphaFold3 can generate a high-quality model, it is likely not a CASP-grade challenge. If it struggles, we want it.

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Alisia Fadini @alisiafadini.bsky.social · 13/03/2026

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 🚀

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Patrick Bryant @patrickbryant1.bsky.social · 07/02/2026

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)

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SBGrid Consortium @sbgrid.bsky.social · 09/01/2026

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.com

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.

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Minhuan Li @minhuanli.bsky.social · 02/01/2026

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)

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cryoEM papers @cryoempapers.bsky.social · 25/11/2025

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

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Alisia Fadini @alisiafadini.bsky.social · 24/11/2025

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

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Cornelius Gati @gati.bsky.social · 05/11/2025

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...

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Mohammed AlQuraishi @moalquraishi.bsky.social · 28/10/2025

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👇

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Alisia Fadini @alisiafadini.bsky.social · 20/10/2025

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!

youtube.com

ROCKET

YouTube video by SBGrid Consortium

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Alisia Fadini @alisiafadini.bsky.social · 02/09/2025

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!! 🚀

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Alisia Fadini @alisiafadini.bsky.social · 24/02/2025

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.

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