iiinova — where your digital self keeps evolving

Reposted by Nicholas Schnicker

Basil Greber @bjgreber.bsky.social · 01/10/2026

Those who had a careful look at the methods section of our work on the #cryoEM structure of the CDK11-cyclin L-SAP30BP complex will have noticed that we added a short peptide to our sample before freezing. If you wonder why...

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Nicholas Schnicker @nschnick.bsky.social · 24/09/2026

I had #Opus5.5 make a demo video (one-shot and also not the real portal/info) to showcase some of the most interesting features! Let me know your thoughts! #StructuralBiology #UIowaResearch #CoreFacility

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Nicholas Schnicker @nschnick.bsky.social · 24/09/2026

It heavily integrates with @globusorg.bsky.social and #CryoSPARC @structurabio.bsky.social to allow for a streamlined user/facility experience.

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Nicholas Schnicker @nschnick.bsky.social · 24/09/2026

easily tracking sample submissions, scoring grids, posting status updates to a user queue, providing updates on live data collections, one-click Globus transfers, and a host of other user/PI/admin portal features.

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Nicholas Schnicker @nschnick.bsky.social · 24/09/2026

Time to share a sneak peek of the #cryoEM portal I've been building for our core with #ClaudeCode and input from Zhen Xu CryoQ is an app that is helping the PSAD Core run our cryoEM microscope more efficiently by...

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Reposted by Nicholas Schnicker

cryoEM papers @cryoempapers.bsky.social · 11/06/2026

Atomic resolution cryo-EM at 200 keV pubmed.ncbi.nlm.nih.gov/42268577/ #cryoEM

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Reposted by Nicholas Schnicker

Biohub @biohub.org · 11/06/2026

In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn

Waves of laser light coming from four different directions and meeting in the middle brightly inside the cavity of the laser phase plate

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Reposted by Nicholas Schnicker

RCSB Protein Data Bank @rcsbpdb.bsky.social · 09/04/2026

RCSB PDB has launched a chatbot to answer general questions about structure deposition, biocuration, validation or PDB policies. Try it today and rate the response: rcsb-deposit-help.rc...

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Nicholas Schnicker @nschnick.bsky.social · 01/04/2026

I couldn’t find info on typical GPU memory usage - do you have a sense of the general requirements?

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Reposted by Nicholas Schnicker

cryoEM papers @cryoempapers.bsky.social · 24/03/2026

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank pubmed.ncbi.nlm.nih.gov/41868252/ #cryoEM

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Reposted by Nicholas Schnicker

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17/03/2026

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

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Reposted by Nicholas Schnicker

John Rubinstein @johnrubinstein.bsky.social · 06/03/2026

I've written a review on what I think is an extremely exciting direction in cryo-EM: Cryo-EM of endogenous membrane proteins in their native lipid bilayer Open access in Quarterly Reviews of Biophysics: doi.org/10.1017/S003...

Figure 1. Cryo-EM of abundant protein complexes in native membranes.

Figure 2. Cryo-EM of membrane proteins in vesicles.

Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.

Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.

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Reposted by Nicholas Schnicker

Bret Freudenthal @freudlab.bsky.social · 03/02/2026

📣 The 2026 Midwest DNA Repair Symposium is coming to Kansas City (registration is open) 🗓 May 30–31, 2026 ✨ Talks will be selected from abstracts, with a strong focus on trainees and new investigators. Please RT & share with your labs! 🔗 sites.google.com/view/kumc-mi...

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Nicholas Schnicker @nschnick.bsky.social · 05/01/2026

As construction of the room for our new Glacios CryoEM comes to an end - here's a quick look at the process. *Not pictured: lots of people to thank, many meetings, phone calls, challenges, delays, and teamwork. I learned a lot during this process - now I'm ready for installation and data collection!

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Reposted by Nicholas Schnicker

Bret Freudenthal @freudlab.bsky.social · 03/11/2025

🎉 Joint paper from the Freudenthal and @tmweaver.bsky.social Labs! Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability. Built on Tyler's foundational work! tinyurl.com/ywkt2bt5

tinyurl.com

Base excision repair in chromatin: A tug-of-war for DNA damage

Base excision repair (BER) is a genome surveillance pathway responsible for repairing DNA base lesions distributed throughout the chromatinized eukary…

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Reposted by Nicholas Schnicker

RCSB Protein Data Bank @rcsbpdb.bsky.social · 27/10/2025

Happening this week! Register for the Thursday October 30 Virtual Office Hour on Structure Summary Pages Learn how a exploring a single PDB structure at RCSB PDB can lead to visualizations, analyses, and searches across the archive

rcsb.org

Learn how a exploring a single PDB structure at RCSB.org can lead to visualizations, analyses, and searches across the archive

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Reposted by Nicholas Schnicker

MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 22/10/2025

Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing Read more: www2.mrc-lmb.cam.ac.uk/a-new-method... #LMBResearch

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Reposted by Nicholas Schnicker

Arc Institute @arcinstitute.org · 24/09/2025

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design. Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

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Nicholas Schnicker @nschnick.bsky.social · 27/08/2025

Love this pipeline! Congrats to all involved!

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Reposted by Nicholas Schnicker

Joshua Weitz @joshuasweitz.bsky.social · 15/08/2025

Major update from #SCIMaP... FY26 House district level scorecards. Our FY26 budget analysis tab includes clickable district info, breaking down the expected economic and job loss given the White House's budget proposal that would slash NIH research funding by >40%. scienceimpacts.org/fy26

scienceimpacts.org

SCIMaP - Impacts of Federal Cuts to Science and Medical Research

View Projected Impact of the FY2026 Budget Cuts to the NIH

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Nicholas Schnicker @nschnick.bsky.social · 13/08/2025

Also curious what the creators @martinpacesa.bsky.social and others use for visualizing results?

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Nicholas Schnicker @nschnick.bsky.social · 13/08/2025

Just made my first webapp mostly for analyzing structures from #BindCraft 👉🏼 pdb-viewer.lovable.app It’s bare 🦴 at this point but curious if others find something like this useful and features they’d like? 🧬🧶

pdb-viewer.lovable.app

Protein Structure Viewer

Upload and interactively visualize multiple Protein Data Bank (.pdb) structures.

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Reposted by Nicholas Schnicker

EMBL-EBI @ebi.embl.org · 07/08/2025

We’ve refreshed the AlphaFold Database Entry Pages! Explore the cleaner design, improved 3D viewer, and easier access from any device 👇 www.alphafold.ebi.ac.uk/entry/P04637 Or read more👇 www.ebi.ac.uk/about/news/u... #AlphaFold #Bioinformatics #UXForScience @pdbeurope.bsky.social

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Reposted by Nicholas Schnicker

cryoEM papers @cryoempapers.bsky.social · 03/08/2025

Affinity-ligand purification of native human low-abundance multi-protein complexes for structure determination www.biorxiv.org/content/10.1101/2025.07.31.667873v1 #cryoEM

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Reposted by Nicholas Schnicker

Jan-Hannes Schaefer @jhschaef.bsky.social · 01/08/2025

Check out our new preprint from the @landerlab.bsky.social, Stagg-Lab and Cianfrocco-Lab: CryoSift - An accessible and automated CNN-driven tool for cryo-EM 2D class selection www.biorxiv.org/content/10.1... Happy testing: cryosift.org #cryoEM #CNN

CryoSift – An accessible and automated CNN-driven
tool for cryo-EM 2D class selection

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Reposted by Nicholas Schnicker

Brittany Trang @brittanytrang.com · 21/07/2025

NEW from me at STAT: We've learned that DeepMind is going to fund CASP, the protein structure competition that brought Google DeepMind's #AlphaFold to prominence (and a Nobel Prize), as its NIH funding runs out. More @statnews.com: www.statnews.com/2025/07/21/c... 🖥️🩺🧪🧬 #bioML

statnews.com

AlphaFold developer Google DeepMind to fund CASP as NIH funding falls short

Protein structure prediction contest CASP gets temporary funding from Google DeepMind as NIH grant runs out.

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Nicholas Schnicker @nschnick.bsky.social · 17/07/2025

Maybe not necessary in your case with high seq identity but also nice since it lets you show the secondary structure alignment as well

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Reposted by Nicholas Schnicker

Waggoner Lab @labwaggoner.bsky.social · 17/07/2025

Designed protein pockets recognize intrinsically disordered protein regions @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... www.statnews.com/2025/07/17/n...

science.org

Disorder meets its match

Designed protein pockets recognize intrinsically disordered protein regions

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Reposted by Nicholas Schnicker

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 02/07/2025

CASP is the main reason the protein structure prediction technology and research field advanced over the last 30 years. And the main reason AI based methods have been accepted and widely applied in biology. So shortsighted of NIH to postpone or even halt funding. John Moult is a scientific hero.

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Reposted by Nicholas Schnicker

Martin Pacesa @martinpacesa.bsky.social · 30/06/2025

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

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Reposted by Nicholas Schnicker

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 19/06/2025

🧪 We're beta testing - and we want your thoughts! Try the redesigned PDBe entry pages & let us know: 🔸 What’s working? 🔸 What’s confusing? 🔸 What features do you miss? 💬 Feedback form: tinyurl.com/pdbe-beta-form #PDBeBeta #Bioinformatics #Biochemistry #Science #UserVoice

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Reposted by Nicholas Schnicker

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 12/06/2025

Fantastic day sharing knowledge with the brilliant researchers at NIH who valiantly work to advance the frontiers of science for the cause of improving human health. Thank you again for your service 🙏 🇺🇸

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Reposted by Nicholas Schnicker

Bret Freudenthal @freudlab.bsky.social · 08/05/2025

The cryo-em core at kumc is looking for a lab manager. This is an exciting opportunity to join a growing facility. kumc.wd5.myworkdayjobs.com/en-US/kumc-j...

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Nicholas Schnicker @nschnick.bsky.social · 07/05/2025

Haha thank you Craig! Of course - you and all the others at PNCC have always been great help!

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Nicholas Schnicker @nschnick.bsky.social · 06/05/2025

Very grateful for all of the support from Iowa colleagues and the Carver College of Medicine in addition to @pacificnwcryoem.bsky.social and the other NIH CryoEM Centers and external university facilities/staff that helped us build a #cryoEM community from the beginning.

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Nicholas Schnicker @nschnick.bsky.social · 06/05/2025

Happy to share we got the NoA for the NIH S10 proposal I submitted for a Glacios #cryoEM 🔬 for #IowaResearch #structuralbiology

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Reposted by Nicholas Schnicker

Dawid Zyla @dzyla.bsky.social · 27/04/2025

1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.

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Reposted by Nicholas Schnicker

SBGrid Consortium @sbgrid.bsky.social · 28/04/2025

11th NIH R25 Train the Trainer SBGrid Consortium workshop at @harvardmed.bsky.social-this one specifically for the #CryoEM Facility leaders. #RELION & #CryoSPARC in @amazonwebservices.bsky.social (AWS) cloud environment. Melissa Chambers & Daniel Stoddard will co-lead the new CryoACCESS initiative.

Photo of workshop attendees standing on the Harvard Quad green in front of Gordon Hall, large stone columned building

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Reposted by Nicholas Schnicker

Jan-Hannes Schaefer @jhschaef.bsky.social · 24/04/2025

Do you want to visualize motion in protein structures? I've used @chimerax.ucsf.edu and little python code to do just that github.com/schaefer-jh/.... Here is some ABC transporter magic. #LLM assisted #coding

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Nicholas Schnicker @nschnick.bsky.social · 22/04/2025

Haha I had just logged into my account to disable messages when it stopped

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Reposted by Nicholas Schnicker

RCSB Protein Data Bank @rcsbpdb.bsky.social · 21/04/2025

Introducing Extended PDB IDs at RCSB PDB Search, view, and download all PDB structures using their extended PDB ID. wwPDB anticipates that all four-character PDB IDs will be exhausted by 2028, after which only 12-character PDB IDs will be issued. www.rcsb.org/news/fe...

rcsb.org

Introducing Extended PDB IDs at RCSB.org

Search, view, and download all PDB structures using their extended PDB ID. wwPDB anticipates that all four-character PDB IDs will be exhausted by 2028, after which only 12-character PDB IDs will be issued.

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