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Ivan Gushchin

@ivangushchin.bsky.social
254 followers 206 following 96 posts

Structural biology and protein engineering

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Ivan Gushchin @ivangushchin.bsky.social · 27/08/2026
Is it possible to find something new in structural biology of ferritins in 2026? Turns out - yes, if it is ferritins from Asgard Archaea! First Cryo-EM structure of a protein for us 🔬🧶
3D model of Asgard dFTN ferritin nanocage
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Structural Biology @actacrystd.iucr.org · 12/08/2026
The photoisomerization of the retinylidene protonated Schiff base in human retinol-binding protein II is described, along with the role of water molecules in this process #ProteinDesign #RhodopsinMimic #SingleCrystalPhotolysis doi.org/10.1107/S205...
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Ivan Gushchin @ivangushchin.bsky.social · 06/08/2026
If you want to do molecular dynamics simulations of carotenoids, look no further: Andrey&Co developed AMBER-compatible parameters for the most common carotenoid moieties
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Edward T Eng @edwardteng.bsky.social · 04/10/2025
Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam. Try the demo here: store.steampowered.com/app/4045010/... Give Muyuan feedback: steamcommunity.com/app/4045010 #ScienceGaming #StructuralBiology #CryoEM #STEMOutreach
store.steampowered.com
Meowtabolism - Examining Feline Behavior within Unicellular Algae on Steam
Explore the interior of an algal cell on your four paws. Built with experimental data and populated with actual protein structures, Meowtabolism offers a glimpse of the vast world inside the basic fun...
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sobolevsky.bsky.social @sobolevsky.bsky.social · 28/05/2026
Happy to share the stepwise mechanism of human TRP channel TRPV6 block by polyamine spermine. Intracellular spermine makes two transient stops in the channel pore before binding to the main site in the selectivity filter. Collaboration with Chubanov and Efremov groups. www.nature.com/articles/s41...
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Martin Pacesa @martinpacesa.bsky.social · 29/04/2026
I am happy to share a review I recently wrote on the design of peptide binders. It gives an overview of experimentally validated tools and discusses the challenges of why peptide design is more difficult than the design of classical protein binders. www.chimia.ch/chimia/artic...
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Martin Pacesa @martinpacesa.bsky.social · 27/04/2026
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GAMA Miguel Angel @miangoar.bsky.social · 20/04/2026
11/12 All the course information, the link to the slides, and more can be found on my site in GithubPages. In addition, YouTube has automatically dubbed the course into 18 other languages to make learning more accessible. I hope you find it useful :) miangoaren.github.io/teaching/pro...
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Martin Pacesa @martinpacesa.bsky.social · 14/04/2026
Really fun and challenging (!) discussion with @cdbahl.com on BindCraft, the state of binder design, the oustanding challenges and perhaps also some misconceptions in the field 💫 www.healthtech.com/the-chain/ma...
healthtech.com
Episode 84 Martin Pacesa on BindCraft An Automated Pipeline for De Novo Protein Binder Design
April 14, 2026 | How is BindCraft, the automated pipeline for de novo protein binder design, changing the protein design industry? Martin Pacesa, assistant professor of pharmacology at the University ...
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Alexey Amunts @amunts.bsky.social · 07/04/2026
65 years after Peter Mitchell’s chemiosmotic theory, we report an association between ATP synthase and the electron transport chain. In the preprint led by @longzhou88.bsky.social, we describe a large supercomplex and show how the supramolecular organization contribute to oxidative phosphorylation 🧵
langtaosha.org.cn
A Supercomplex Incorporating Both Electron Transport Chain and ATP Synthase
The mitochondrial oxidative phosphorylation system powering most aerobic organisms is typically depicted as two spatially segregated machineries(1): electron transport chain complexes I-IV (ETC CI-CIV
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Egor Marin @marinegor.bsky.social · 30/03/2026
Rarely show my work stuff here, but we did something cool (and open-source!) last week: github.com/ENPICOM/immu... TL;DR: - antibody numbering and segmentation with Rust - bindings to python, polars and WASM - VERY fast numbering at scale (got up to 1,000,000 seqs per second on 48 CPUs)
github.com
GitHub - ENPICOM/immunum: A high-performance antibody and TCR sequence numbering tool for Rust, Python, Polars and JS/TS.
A high-performance antibody and TCR sequence numbering tool for Rust, Python, Polars and JS/TS. - ENPICOM/immunum
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Hideaki E. Kato @emekato.bsky.social · 11/03/2026
Happy to share our work on conventional and time-resolved cryo-EM studies of NTSR1, now published in Nature! nature.com/articles/s41... Wonderful collab. w/ Sumino, Mitsutake, Kobilka, & Inoue labs. Congrats to Kazuhiro, Kouki, Toshiki, Shun & everyone involved!
nature.com
The dynamic basis of G-protein recognition and activation by a GPCR - Nature
Conventional and time-resolved cryo-electron microscopy reveal how NTSR1 dynamically engages and releases different G proteins, capturing over 20 intermediates and uncovering key mechanistic step...
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Ivan Gushchin @ivangushchin.bsky.social · 07/03/2026
In situ Cryo-EM: study proteins in physiological environment!
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Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 20/02/2026
Started this project years ago, but now everything is deposited on @addgene.bsky.social and a short @protocolsio.bsky.social is online. Try it out to make your own (cheap) homemade nuclease/Benzonase! dx.doi.org/10.17504/protocols.io.261ged7xov47/v2 Thank you @jcoker10.bsky.social and Michael Lim!
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Ivan Gushchin @ivangushchin.bsky.social · 19/02/2026
New preprint: We checked whether AlphaFold and its great freely available analogs (including the recent Protenix) can predict the effects of ligand charge. Surprisingly, the predictions sometimes depended on the input format stronger than on the charge! (1/6)
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AI x Bio Discovery @aixbiobot.bsky.social · 19/02/2026
Influence of molecular representation and charge on protein-ligand structural predictions by popular co-folding methods [new] Input format impacts pred's more than protonation. Consistency & protonation steps vital for model improv.
Influence of molecular representation and charge on protein-ligand structural predictions by popular co-folding methodsFigure 1Figure 2Figure 3
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Ivan Gushchin @ivangushchin.bsky.social · 12/02/2026
I found it very interesting to surf gene neighborhoods of homologs to the proteins we study
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Igor Jouline @jouline.bsky.social · 12/02/2026
A ligand-binding sensor domain got a tiny insertion from cytochrome c, which contained a heme-binding motif, and now it is a nitric oxide sensor. As simple as that: www.biorxiv.org/content/10.6...
biorxiv.org
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Alexey Amunts @amunts.bsky.social · 06/02/2026
We're launching a research lab at SMART. Shenzhen Medical Academy for Research and Translation is a newly established institute with long-term funding mechanisms for internal and external investigators. At full capacity SMART aims to support up to 400 labs. www.scmp.com/news/china/s...
scmp.com
Structural biologist Alexey Amunts launches new research lab in Shenzhen
‘Shenzhen adds another dimension; it is a place where ideas do not remain ideas for long,’ Amunts says of new position.
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GAMA Miguel Angel @miangoar.bsky.social · 03/02/2026
I recorded ~8h introducing the main algorithms for protein design: from classical approaches to protein language models, AlphaFold, ESMFold, MPNN, diffusion models and more :) youtu.be/wKUYtAt87d4T... Slides drive.google.com/file/d/1EPLj... English is available only via auto-translated subtitles
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BWJones @bwjones.bsky.social · 03/02/2026
The bureaucracy of science has grown so much, the system is collapsing upon itself: Scientists have become administrators of grants rather than spending time on science. Paid administrators are demanding even more administrative work from scientists. Administrators are eating the science budget.
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GAMA Miguel Angel @miangoar.bsky.social · 02/02/2026
I’ve recorded ~8h explaining the architectures of AlphaFold, AF2 & AF3, as well as the context needed to understand their development, applications and limitations :) youtu.be/_jDRr5BcTaY Slides drive.google.com/file/d/1i4QE... English is available only via auto-translated subtitles
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Verena Resch | 🧪🖥️ @verenaresch.bsky.social · 23/12/2025
As the year winds down, I hope you all get the chance to slow down, spend time with family and loved ones, and enjoy the simple moments. I wish you a warm and peaceful holiday season 💫
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Johannes Vierock @johvierock.bsky.social · 22/12/2025
Four years ago, the red-light–activated channelrhodopsin #Chrimson restored basic vision in a blind patient. Here, we uncover its #multicolor_photoreactions and show implications for optogenetic applications. Many interesting details and a wonderful team🥳! www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Ivan Gushchin @ivangushchin.bsky.social · 20/12/2025
Given the "positive inside" rule, many membrane proteins could potentially interact with negatively charged nucleic acids - I wonder if anyone done a whole proteome analysis
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Oli Clarke @olibclarke.bsky.social · 18/12/2025
very unusual - a tRNA regulated anion channel
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Ivan Gushchin @ivangushchin.bsky.social · 16/12/2025
Bacteriorhodopsin is not from bacteria 😅
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Ivan Gushchin @ivangushchin.bsky.social · 06/12/2025
Cryo-EM structure of sensor histidine kinase QseE with its activator QseG. Once again AlphaFold produced great model for the complex before the experimental data were available! doi.org/10.1128/mbio...
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Ivan Gushchin @ivangushchin.bsky.social · 03/12/2025
Hall of Fame for unexpected Boltz predictions, by Pavel Shishkin
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Ivan Gushchin @ivangushchin.bsky.social · 03/12/2025
Joys of correcting proofs
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Misha Kudryashev @mishakudryashev.bsky.social · 21/11/2025
We got a large Helmholtz Bioengineering grant with Oliver Daumke, Artur Yakimovich, Alina Bazarova, and Dietrich Ruess to use protein design to target cancer. Five open postdoctoral positions in Generative AI & Protein Engineering. Share & apply! jobrxiv.org/job/max-delb...
jobrxiv.org
Postdoctoral Positions in Protein Engineering
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
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Elodie Laine @laineelodie.bsky.social · 10/11/2025
Our new special collection "Protein-Nucleic Acid Interactions: From Origins to Design (2025)" is now published in Current Opinion in Structural Biology. I'm excited to have both co-edited it with Shandar Ahmad and contributed a review! www.sciencedirect.com/special-issu...
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Ivan Gushchin @ivangushchin.bsky.social · 31/10/2025
Great work! Always wanted to do this myself
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Alexey Amunts @amunts.bsky.social · 31/10/2025
What a gem from @dudinlab.bsky.social @gautamdey.bsky.social @centriolelab.bsky.social in Cell! Expansion microscopy atlas of >200 eukaryotes comparing cytoskeletal architectures revealing structures not seen before. Stunning visualisation! Exactly the kind of transformative cell biology we need.
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sobolevsky.bsky.social @sobolevsky.bsky.social · 24/10/2025
www.nature.com/articles/s41...
nature.com
Structural basis for agonist and heat activation of nociceptor TRPM3 - Nature Structural & Molecular Biology
TRPM3 is an ion channel that helps the body sense heat and contributes to pain. The authors show that both heat and small chemical molecules switch it on through similar changes inside the protein.
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Joe Greener @jgreener64.bsky.social · 15/10/2025
I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...
jgreener64.github.io
Where next for structural bioinformatics?
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Ivan Gushchin @ivangushchin.bsky.social · 16/10/2025
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Ivan Gushchin @ivangushchin.bsky.social · 06/10/2025
Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout
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Ivan Gushchin @ivangushchin.bsky.social · 01/10/2025
Glad to contribute to this: in our most recent preprint, we describe peculiar ferritin-like proteins that have ferroxidase activity, but do not form shells, using encapsulin compartments instead: doi.org/10.1101/2025...
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Richard Sever @richardsever.bsky.social · 01/10/2025
Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵
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piatkevich.bsky.social @piatkevich.bsky.social · 15/09/2025
Major milestone for WeKwikGene! wekwikgene.wllsb.edu.cn now features 1,000+ ready-to-ship plasmids with 800+ more plasmids under QC. We've processed 1,000+ requests & distributed 3,000+ plasmids worldwide.
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BejaLabTechnion @bejalab.bsky.social · 08/09/2025
Structural basis for no retinal binding in flotillin-associated rhodopsins www.cell.com/structure/fu...
cell.com
Structural basis for no retinal binding in flotillin-associated rhodopsins
Kovalev et al. determined cryo-EM structures of a flotillin-associated rhodopsin (FAR) lacking retinal cofactor and its retinal-binding paralog, a classical light-driven proton pump from the same bact...
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Niko McCarty @nikomccarty.bsky.social · 01/09/2025
Out today: A useful review on AI-designed protein binders. It covers the history of this work + has lots of good case studies, including how these tools are being used to make snake anti-venoms. The tables are particularly valuable.
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Miguel Matilla - Matilla Lab @miguelmatilla.bsky.social · 01/09/2025
Neurotransmitters guide the chemotaxis behavior of the global human pathogen Pseudomonas aeruginosa. Discover more in our new article at @microbiotech.bsky.social @blastmeetings.bsky.social @eezcsic.bsky.social @csicdivulga.bsky.social @krelllaboratory.bsky.social dx.doi.org/10.1111/1751...
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Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...
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Boston Protein Design and Modeling Club @bpdmc.org · 15/08/2025
Have no fear if you weren't in the packed audience this week for @martinpacesa.bsky.social's awesome seminar, because you can check out the recording 👇 youtu.be/qQihl6If9vU
youtu.be
BindCraft: one-shot design of functional protein binders
YouTube video by Boston Protein Design and Modeling Club
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Ivan Gushchin @ivangushchin.bsky.social · 11/08/2025
Got an idea while reviewing a grant and a paper Image courtesy: Qwen
A thought on using AI for peer review: instead of avoiding or discouraging it, the systems used for submission and evaluation should explicitly provide the authors, and then the reviewers with a thorough LLM evaluation. This will help in weeding out basic logical flaws and typos, and provide the human reviewers with a list of points which they can either confirm or disregard, and then add what was missed by the AI.

Yes, LLMs don't have access to subscription-based publications or field insider knowledge - that's what the human reviewers are needed for.  

Also, everyone is using LLMs anyway, why not make it explicit and to the highest standard possible, with the best prompts and LLM models.
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Ivan Gushchin @ivangushchin.bsky.social · 21/07/2025
Summer holidays @natcomms.nature.com ? 😕
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Ivan Gushchin @ivangushchin.bsky.social · 20/07/2025
Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications
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The Align Foundation @alignbio.bsky.social · 08/07/2025
1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience
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