Fernando Bazan
@jfernandobazan.bsky.social
curious about all things bio & solving tricky structural puzzles / mlbio for protein design, engineering & drug disco / cytokine immunologist / stanfordberkelyucsf & dnaxgenentech / recovering twit
Reposted by Fernando Bazan
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
Reposted by Fernando Bazan
Reposted by Fernando Bazan
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Reposted by Fernando Bazan
October 28, 2025 at 3:34 AM
Reposted by Fernando Bazan
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
October 20, 2025 at 11:26 AM
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs
📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
Reposted by Fernando Bazan
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Reposted by Fernando Bazan
Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Structural basis of T-loop–independent recognition and activation of CDKs by the CDK-activating kinase
Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation o...
www.science.org
October 16, 2025 at 7:17 PM
Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Fernando Bazan
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
The functional landscape of the human ubiquitinome
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...
www.biorxiv.org
October 9, 2025 at 7:07 AM
new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
Reposted by Fernando Bazan
How do SMC complexes load onto DNA to get ready for loop extrusion?
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
October 9, 2025 at 2:43 PM
How do SMC complexes load onto DNA to get ready for loop extrusion?
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
Reposted by Fernando Bazan
Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...
Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail
This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.
www.science.org
October 6, 2025 at 11:31 AM
Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...
Reposted by Fernando Bazan
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 2, 2025 at 3:01 AM
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Check out this work co-led with @benadler.bsky.social here:
www.nature.com/articles/s41...
Reposted by Fernando Bazan
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
www.nature.com
October 1, 2025 at 4:05 PM
Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
Reposted by Fernando Bazan
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 1, 2025 at 5:57 PM
Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...
Reposted by Fernando Bazan
Elaborate machinery for inserting proteins into the outer membrane of bacteria www.nature.com/articles/d41...
Elaborate machinery for inserting proteins into the outer membrane of bacteria
Bacteria in the gut use an unusual molecular apparatus to insert complex proteins into their outer membrane.
www.nature.com
October 2, 2025 at 9:29 AM
Elaborate machinery for inserting proteins into the outer membrane of bacteria www.nature.com/articles/d41...
Reposted by Fernando Bazan
The Bridge ~ Valerie Thornton, 1954
September 30, 2025 at 8:43 PM
The Bridge ~ Valerie Thornton, 1954
Reposted by Fernando Bazan
Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes.
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology
imageimagehu.MAP3.0 integrates mass spectrometry experiments to identify human protein complexes.
Using this resource, this study characterizes covariation of complexes, identifies
mutually exclusive ...
www.embopress.org
May 29, 2025 at 11:24 PM
Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes.
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Reposted by Fernando Bazan
Thrilled to share our new Science paper!
Predicting protein-protein interactions in the human proteome | Science www.science.org/doi/10.1126/...
Predicting protein-protein interactions in the human proteome | Science www.science.org/doi/10.1126/...
Predicting protein-protein interactions in the human proteome
Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identificatio...
www.science.org
September 27, 2025 at 6:31 PM
Thrilled to share our new Science paper!
Predicting protein-protein interactions in the human proteome | Science www.science.org/doi/10.1126/...
Predicting protein-protein interactions in the human proteome | Science www.science.org/doi/10.1126/...
Reposted by Fernando Bazan
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for
>4,400 viruses, allowing mapping of form and function across the human and animal
virosphere. Viro3D i...
www.embopress.org
September 28, 2025 at 5:39 AM
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Reposted by Fernando Bazan
Cryo-EM captures the elusive moment when E1 hands off SUMO to E2- a molecular relay that’s been mostly guesswork until now. The structures reveal E1 doing dramatic shape-shifting to line up perfectly for the transfer, like enzyme origami in action.
New online: Cryo-EM structures reveal the molecular mechanism of SUMO E1–E2 thioester transfer
Cryo-EM structures reveal the molecular mechanism of SUMO E1–E2 thioester transfer
Nature Structural & Molecular Biology, Published online: 25 September 2025; doi:10.1038/s41594-025-01681-8This study reveals how human small ubiquitin-like modifier (SUMO) E1 recruits its E2 partner UBC9 and transfers SUMO1 through large structural changes, uncovering key mechanisms that ensure specificity and fidelity in SUMOylation, an essential protein modification pathway.
go.nature.com
September 28, 2025 at 6:43 PM
Cryo-EM captures the elusive moment when E1 hands off SUMO to E2- a molecular relay that’s been mostly guesswork until now. The structures reveal E1 doing dramatic shape-shifting to line up perfectly for the transfer, like enzyme origami in action.
Reposted by Fernando Bazan
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
doi.org/10.1101/2025.09.24.678028 #proteindesign
September 28, 2025 at 9:16 PM
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
doi.org/10.1101/2025.09.24.678028 #proteindesign
Reposted by Fernando Bazan
"Les Bibliophiles, journée d'automne à Paris"
1925
Christopher Richard Wynne Nevinson
(1889-1946)
was a British painter, printmaker and lithographer.
#art #painting #painters #BlueSkyArt
1925
Christopher Richard Wynne Nevinson
(1889-1946)
was a British painter, printmaker and lithographer.
#art #painting #painters #BlueSkyArt
September 27, 2025 at 8:01 PM
"Les Bibliophiles, journée d'automne à Paris"
1925
Christopher Richard Wynne Nevinson
(1889-1946)
was a British painter, printmaker and lithographer.
#art #painting #painters #BlueSkyArt
1925
Christopher Richard Wynne Nevinson
(1889-1946)
was a British painter, printmaker and lithographer.
#art #painting #painters #BlueSkyArt
Reposted by Fernando Bazan
open.substack.com/pub/genomely... Another write up on the recently published Simplefold by @apple
SimpleFold and the Future of Protein Folding
A Generative Shift in Protein Folding
open.substack.com
September 27, 2025 at 3:35 PM
open.substack.com/pub/genomely... Another write up on the recently published Simplefold by @apple
Reposted by Fernando Bazan
🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses.
🔗 viro3d.cvr.gla.ac.uk
📄 www.embopress.org/doi/full/10....
@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
🔗 viro3d.cvr.gla.ac.uk
📄 www.embopress.org/doi/full/10....
@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
Viro3D
viro3d.cvr.gla.ac.uk
September 26, 2025 at 11:36 AM
🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses.
🔗 viro3d.cvr.gla.ac.uk
📄 www.embopress.org/doi/full/10....
@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
🔗 viro3d.cvr.gla.ac.uk
📄 www.embopress.org/doi/full/10....
@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
Reposted by Fernando Bazan
Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity i...
www.biorxiv.org
September 22, 2025 at 1:28 PM
Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Fernando Bazan
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾
🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture.
buff.ly/j3TSIkn
buff.ly/j3TSIkn
September 20, 2025 at 7:24 PM
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾