Ivan Gushchin
@ivangushchin.bsky.social
Structural biology and protein engineering
Pinned
Ivan Gushchin
@ivangushchin.bsky.social
· Nov 22
We engineered bacteriorhodopsin to be soluble. It binds retinal and can photocycle! X-ray structure reveals conserved binding pocket with 0.8 Å all atom RMSD to WT BR. All this became possible due to hard work by Andrey Nikolaev and the team 🙏 #proteindesign biorxiv.org/cgi/content/...
Reposted by Ivan Gushchin
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...
Five open postdoctoral positions in Generative AI & Protein Engineering. Share & apply!
jobrxiv.org/job/max-delb...
Postdoctoral Positions in Protein Engineering
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
November 21, 2025 at 7:08 AM
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...
Five open postdoctoral positions in Generative AI & Protein Engineering. Share & apply!
jobrxiv.org/job/max-delb...
Reposted by Ivan Gushchin
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...
www.sciencedirect.com/special-issu...
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
November 10, 2025 at 5:54 PM
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...
www.sciencedirect.com/special-issu...
Great work! Always wanted to do this myself
Design stable, folded proteins using only the 10 "ancient" amino acids.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 31, 2025 at 8:22 PM
Great work! Always wanted to do this myself
Reposted by Ivan Gushchin
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.
October 31, 2025 at 5:45 PM
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.
Reposted by Ivan Gushchin
Reposted by Ivan Gushchin
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...
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...
Where next for structural bioinformatics?
jgreener64.github.io
October 15, 2025 at 2:16 PM
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...
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...
Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout
October 6, 2025 at 6:23 AM
Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout
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...
October 1, 2025 at 7:36 PM
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...
Reposted by Ivan Gushchin
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 🫵
October 1, 2025 at 3:51 PM
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 🫵
Reposted by Ivan Gushchin
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.
September 15, 2025 at 2:58 AM
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.
Reposted by Ivan Gushchin
Structural basis for no retinal binding in flotillin-associated rhodopsins www.cell.com/structure/fu...
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...
www.cell.com
September 8, 2025 at 4:24 AM
Structural basis for no retinal binding in flotillin-associated rhodopsins www.cell.com/structure/fu...
Reposted by Ivan Gushchin
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.
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.
September 1, 2025 at 6:54 PM
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.
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.
Reposted by Ivan Gushchin
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...
dx.doi.org/10.1111/1751...
September 1, 2025 at 11:18 AM
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...
dx.doi.org/10.1111/1751...
Reposted by Ivan Gushchin
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...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
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...
www.nature.com/articles/s41...
Reposted by Ivan Gushchin
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/qQihl6If9vU
BindCraft: one-shot design of functional protein binders
YouTube video by Boston Protein Design and Modeling Club
youtu.be
August 15, 2025 at 8:56 PM
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/qQihl6If9vU
Got an idea while reviewing a grant and a paper
Image courtesy: Qwen
Image courtesy: Qwen
August 11, 2025 at 9:35 AM
Got an idea while reviewing a grant and a paper
Image courtesy: Qwen
Image courtesy: Qwen
Summer holidays @natcomms.nature.com ? 😕
July 21, 2025 at 3:10 PM
Summer holidays @natcomms.nature.com ? 😕
Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications
July 20, 2025 at 9:55 AM
Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications
Reposted by Ivan Gushchin
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
🚀 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
July 8, 2025 at 4:26 PM
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
🚀 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
Reposted by Ivan Gushchin
For high-resolution studies of intracellular crystals, in-house electron diffraction methods are shown to be orders of magnitude more efficient than serial X-ray crystallography regarding the total crystal material required and the radiation dose deposited.
July 14, 2025 at 10:26 AM
For high-resolution studies of intracellular crystals, in-house electron diffraction methods are shown to be orders of magnitude more efficient than serial X-ray crystallography regarding the total crystal material required and the radiation dose deposited.
Reposted by Ivan Gushchin
This paper is absolutely bananas and a tour de force of structural bioinformatics. Some random tidbits:
NEW pub: The role of metabolism in shaping #enzyme structures over 400 million years. Now out in @nature.com
Super grateful to have played a small role in this project - congrats to lead/corr authors Oliver, Benjamin, and Markus!
www.nature.com/articles/s41...
#alphafold #evolution #genomics
Super grateful to have played a small role in this project - congrats to lead/corr authors Oliver, Benjamin, and Markus!
www.nature.com/articles/s41...
#alphafold #evolution #genomics
July 14, 2025 at 6:15 PM
This paper is absolutely bananas and a tour de force of structural bioinformatics. Some random tidbits:
Interesting work from my former lab mate Vitaly Polovinkin and colleagues: solving a high resolution structure of a protein inside the cell using electron diffraction
July 12, 2025 at 12:08 PM
Interesting work from my former lab mate Vitaly Polovinkin and colleagues: solving a high resolution structure of a protein inside the cell using electron diffraction
Reposted by Ivan Gushchin
***JOB OFFER***
The Protein Design and Modeling lab at IBMB offers a postdoc position at the intersection of computational protein design, biophysics and structural biology. Please share with colleagues and anyone you know that might be interested.
ibmb.csic.es/en/jobs/post...
The Protein Design and Modeling lab at IBMB offers a postdoc position at the intersection of computational protein design, biophysics and structural biology. Please share with colleagues and anyone you know that might be interested.
ibmb.csic.es/en/jobs/post...
July 11, 2025 at 8:49 AM
***JOB OFFER***
The Protein Design and Modeling lab at IBMB offers a postdoc position at the intersection of computational protein design, biophysics and structural biology. Please share with colleagues and anyone you know that might be interested.
ibmb.csic.es/en/jobs/post...
The Protein Design and Modeling lab at IBMB offers a postdoc position at the intersection of computational protein design, biophysics and structural biology. Please share with colleagues and anyone you know that might be interested.
ibmb.csic.es/en/jobs/post...
Reposted by Ivan Gushchin
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...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
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...
github.com/martinpacesa...