David Gomez Navarro
@gomeznavarro.bsky.social
PhD Student #StructuralBiology #CryoET
Reposted by David Gomez Navarro
SRBD1, a highly conserved gene required for chromosome individualization
SRBD1, a highly conserved gene required for chromosome individualization
Raaijmakers et al. study S1 domain containing protein 1 (SRBD1), a previously uncharacterized essential protein. The loss of SRBD1 results in a complete failure in anaphase chromosome segregation due to defects established in prophase. The phenotype…
dlvr.it
March 19, 2025 at 11:23 PM
SRBD1, a highly conserved gene required for chromosome individualization
Reposted by David Gomez Navarro
New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴
doi.org/10.48550/arX...
doi.org/10.48550/arX...
September 17, 2025 at 4:17 PM
New review on computational design of intrinsically disordered proteins 🖥️🍝 by @giuliotesei.bsky.social @fpesce.bsky.social & 👴
doi.org/10.48550/arX...
doi.org/10.48550/arX...
Reposted by David Gomez Navarro
Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8)
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
September 30, 2025 at 9:55 PM
Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8)
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Reposted by David Gomez Navarro
Excited to share our latest work in expanding AI-based protein design into targeting PTMs! I’m particularly excited in this work as there is so much we don’t know about PTMs despite their central role in signaling and hopefully we can start to decode their rules and functions.
Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8)
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
September 30, 2025 at 11:42 PM
Excited to share our latest work in expanding AI-based protein design into targeting PTMs! I’m particularly excited in this work as there is so much we don’t know about PTMs despite their central role in signaling and hopefully we can start to decode their rules and functions.
Reposted by David Gomez Navarro
La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
September 11, 2025 at 8:23 AM
La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
Reposted by David Gomez Navarro
Train a protein structure predictor that can handle 29 non-canonical amino acids, then use it to design binders with non-canonical amino acids that reduce immunogenicity.
@panhammarstrom.bsky.social @patrickbryant1.bsky.social
www.biorxiv.org/content/10.1...
@panhammarstrom.bsky.social @patrickbryant1.bsky.social
www.biorxiv.org/content/10.1...
September 9, 2025 at 8:03 PM
Train a protein structure predictor that can handle 29 non-canonical amino acids, then use it to design binders with non-canonical amino acids that reduce immunogenicity.
@panhammarstrom.bsky.social @patrickbryant1.bsky.social
www.biorxiv.org/content/10.1...
@panhammarstrom.bsky.social @patrickbryant1.bsky.social
www.biorxiv.org/content/10.1...
Reposted by David Gomez Navarro
📢 Ready for this? A new way to think about Gene Regulation!
🚨A new coregulator complex, Zincore, acts as a "MOLECULAR GRIP", stabilizing TFs at DNA binding sites across the genome!🧬
💪Proud to be part of this work led by @daaninthelab.bsky.social
Read more: science.org/doi/10.1126/science.adv2861
🚨A new coregulator complex, Zincore, acts as a "MOLECULAR GRIP", stabilizing TFs at DNA binding sites across the genome!🧬
💪Proud to be part of this work led by @daaninthelab.bsky.social
Read more: science.org/doi/10.1126/science.adv2861
July 8, 2025 at 11:18 AM
📢 Ready for this? A new way to think about Gene Regulation!
🚨A new coregulator complex, Zincore, acts as a "MOLECULAR GRIP", stabilizing TFs at DNA binding sites across the genome!🧬
💪Proud to be part of this work led by @daaninthelab.bsky.social
Read more: science.org/doi/10.1126/science.adv2861
🚨A new coregulator complex, Zincore, acts as a "MOLECULAR GRIP", stabilizing TFs at DNA binding sites across the genome!🧬
💪Proud to be part of this work led by @daaninthelab.bsky.social
Read more: science.org/doi/10.1126/science.adv2861
Reposted by David Gomez Navarro
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 David Gomez Navarro
Nature research paper: One-shot design of functional protein binders with BindCraft
go.nature.com/46bhOAv
go.nature.com/46bhOAv
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
go.nature.com
September 1, 2025 at 5:37 PM
Nature research paper: One-shot design of functional protein binders with BindCraft
go.nature.com/46bhOAv
go.nature.com/46bhOAv
Reposted by David Gomez Navarro
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 David Gomez Navarro
Excited to share that our paper on mitochondrial cardiolipin dynamics is published in @natcomms.nature.com today! We provide molecular explanations for unique aspects of mitochondrial morphology and the mechanisms underlying cardiolipin-related Barth Syndrome.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cardiolipin dynamics promote membrane remodeling by mitochondrial OPA1 - Nature Communications
This study reveals how cardiolipin governs mitochondrial morphology by modulating the activity of human OPA1 and how its replacement by monolyso-cardiolipin, as observed in Barth syndrome, impacts mitochondrial membrane-shaping mechanisms.
www.nature.com
September 30, 2025 at 8:09 PM
Excited to share that our paper on mitochondrial cardiolipin dynamics is published in @natcomms.nature.com today! We provide molecular explanations for unique aspects of mitochondrial morphology and the mechanisms underlying cardiolipin-related Barth Syndrome.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by David Gomez Navarro
🚨New Article Out!!
📢 In our latest work, we propose a Three-Point Lock binding mode for ATX inhibitors 🔒
🚀 This approach may represent the final piece in the puzzle of known binding mode types — and could have therapeutic relevance
♥️ Thanks for your support
Read more here: doi.org/10.1016/j.bm...
📢 In our latest work, we propose a Three-Point Lock binding mode for ATX inhibitors 🔒
🚀 This approach may represent the final piece in the puzzle of known binding mode types — and could have therapeutic relevance
♥️ Thanks for your support
Read more here: doi.org/10.1016/j.bm...
April 15, 2025 at 11:24 PM
🚨New Article Out!!
📢 In our latest work, we propose a Three-Point Lock binding mode for ATX inhibitors 🔒
🚀 This approach may represent the final piece in the puzzle of known binding mode types — and could have therapeutic relevance
♥️ Thanks for your support
Read more here: doi.org/10.1016/j.bm...
📢 In our latest work, we propose a Three-Point Lock binding mode for ATX inhibitors 🔒
🚀 This approach may represent the final piece in the puzzle of known binding mode types — and could have therapeutic relevance
♥️ Thanks for your support
Read more here: doi.org/10.1016/j.bm...
Reposted by David Gomez Navarro
🚨 New strategy against colorectal cancer!
Dual GSK-3 & BCL-XL inhibition kills APC-mutant cells in organoid models, tipping the balance towards healthy cells—a promising way to halt early tumor growth 💪🧪
➡️Read more: www.nature.com/articles/s41...
Dual GSK-3 & BCL-XL inhibition kills APC-mutant cells in organoid models, tipping the balance towards healthy cells—a promising way to halt early tumor growth 💪🧪
➡️Read more: www.nature.com/articles/s41...
GSK-3 and BCL-XL inhibition mitigates the competitive advantage of APC-mutant colorectal cancer cells - Oncogenesis
Oncogenesis - GSK-3 and BCL-XL inhibition mitigates the competitive advantage of APC-mutant colorectal cancer cells
www.nature.com
July 15, 2025 at 9:39 AM
🚨 New strategy against colorectal cancer!
Dual GSK-3 & BCL-XL inhibition kills APC-mutant cells in organoid models, tipping the balance towards healthy cells—a promising way to halt early tumor growth 💪🧪
➡️Read more: www.nature.com/articles/s41...
Dual GSK-3 & BCL-XL inhibition kills APC-mutant cells in organoid models, tipping the balance towards healthy cells—a promising way to halt early tumor growth 💪🧪
➡️Read more: www.nature.com/articles/s41...
Reposted by David Gomez Navarro
📢 Excited to announce that our Opinion paper on GPI-anchored proteins is now Published! 🎉
👀 If you're working in this field, be sure to check out our paper — we've highlighted some truly outstanding questions on the topic! ⚠️
www.cell.com/trends/cell-...
👀 If you're working in this field, be sure to check out our paper — we've highlighted some truly outstanding questions on the topic! ⚠️
www.cell.com/trends/cell-...
January 23, 2025 at 10:09 PM
📢 Excited to announce that our Opinion paper on GPI-anchored proteins is now Published! 🎉
👀 If you're working in this field, be sure to check out our paper — we've highlighted some truly outstanding questions on the topic! ⚠️
www.cell.com/trends/cell-...
👀 If you're working in this field, be sure to check out our paper — we've highlighted some truly outstanding questions on the topic! ⚠️
www.cell.com/trends/cell-...
Reposted by David Gomez Navarro
In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11
Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression
Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...
www.science.org
July 4, 2025 at 11:00 AM
In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11
Reposted by David Gomez Navarro
👀 Just updated my Google Scholar and... can’t believe one of my papers reached 100 citations! 🚀
💪🏼 It might not seem like much, but as a PhD student, it feels like a big achievement.
❤️ To all fellow PhDs, keep going, stay strong, and celebrate every milestone!🔁
Read it: www.jbc.org/article/S002...
💪🏼 It might not seem like much, but as a PhD student, it feels like a big achievement.
❤️ To all fellow PhDs, keep going, stay strong, and celebrate every milestone!🔁
Read it: www.jbc.org/article/S002...
July 15, 2025 at 10:50 PM
👀 Just updated my Google Scholar and... can’t believe one of my papers reached 100 citations! 🚀
💪🏼 It might not seem like much, but as a PhD student, it feels like a big achievement.
❤️ To all fellow PhDs, keep going, stay strong, and celebrate every milestone!🔁
Read it: www.jbc.org/article/S002...
💪🏼 It might not seem like much, but as a PhD student, it feels like a big achievement.
❤️ To all fellow PhDs, keep going, stay strong, and celebrate every milestone!🔁
Read it: www.jbc.org/article/S002...
Reposted by David Gomez Navarro
This is an enormous accomplishment
Proud of new work tinyurl.com/yhz4c6ry from the lab by Zhicheng (Chen) Cui using single-particle cryo-EM on liposomes to show how mTORC1 integrates nutrient and growth factor signaling at lysosomes, collab. w/
G. Napolitano,A. Esposito, and A. Ballabio.
G. Napolitano,A. Esposito, and A. Ballabio.
November 17, 2024 at 12:19 AM
This is an enormous accomplishment
Reposted by David Gomez Navarro
AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔
➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!
🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...
➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!
🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...
November 5, 2024 at 12:18 AM
AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔
➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!
🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...
➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!
🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...
Reposted by David Gomez Navarro
🚀 Excited about our pre-print:
AlphaBridge: A User-Friendly Tool for Interpreting Protein Predictions
Whether you're an expert or just new to the field of Protein Prediction, AlphaBridge is the way to go!
🔁Try it and share your thoughts!
📜 Article: www.biorxiv.org/content/10.1...
AlphaBridge: A User-Friendly Tool for Interpreting Protein Predictions
Whether you're an expert or just new to the field of Protein Prediction, AlphaBridge is the way to go!
🔁Try it and share your thoughts!
📜 Article: www.biorxiv.org/content/10.1...
October 28, 2024 at 7:03 PM
🚀 Excited about our pre-print:
AlphaBridge: A User-Friendly Tool for Interpreting Protein Predictions
Whether you're an expert or just new to the field of Protein Prediction, AlphaBridge is the way to go!
🔁Try it and share your thoughts!
📜 Article: www.biorxiv.org/content/10.1...
AlphaBridge: A User-Friendly Tool for Interpreting Protein Predictions
Whether you're an expert or just new to the field of Protein Prediction, AlphaBridge is the way to go!
🔁Try it and share your thoughts!
📜 Article: www.biorxiv.org/content/10.1...
Reposted by David Gomez Navarro
Let's bring the #CellDeath community together here on 🦋
Just get in touch to join this Starter Pack
go.bsky.app/R6mGrKU
Just get in touch to join this Starter Pack
go.bsky.app/R6mGrKU
November 16, 2024 at 9:41 AM
Let's bring the #CellDeath community together here on 🦋
Just get in touch to join this Starter Pack
go.bsky.app/R6mGrKU
Just get in touch to join this Starter Pack
go.bsky.app/R6mGrKU
Reposted by David Gomez Navarro
November 8, 2024 at 10:01 PM
Reposted by David Gomez Navarro
How does one combine single particle cryo-EM ❄️🔬 and EELS 🌈 to REEL-EM (Reconstructed Electron Energy-Loss - Elemental Mapping) to reconstruct elemental signatures in the 3D space of protein complexes? Take a look here: www.nature.com/articles/s41...
Elemental mapping in single-particle reconstructions by reconstructed electron energy-loss analysis - Nature Methods
An approach combining electron energy-loss spectroscopy with image processing tools from single-particle cryo-electron microscopy enables elemental mapping in macromolecular complexes, paving the way ...
www.nature.com
November 14, 2024 at 7:29 PM
How does one combine single particle cryo-EM ❄️🔬 and EELS 🌈 to REEL-EM (Reconstructed Electron Energy-Loss - Elemental Mapping) to reconstruct elemental signatures in the 3D space of protein complexes? Take a look here: www.nature.com/articles/s41...
Reposted by David Gomez Navarro
Sounds like an amazing project!
And bonus: It's Ribosomes !!! ;)
And bonus: It's Ribosomes !!! ;)
We offer two fully-funded PhD studentships to investigate ribosome hibernation in stem cells via cryoET. If you are interested, please apply here: www.exeter.ac.uk/research/ins...
or here: www.exeter.ac.uk/study/fundin.... If you have any questions, do not hesitate to get in touch!
or here: www.exeter.ac.uk/study/fundin.... If you have any questions, do not hesitate to get in touch!
November 15, 2024 at 4:59 PM
Sounds like an amazing project!
And bonus: It's Ribosomes !!! ;)
And bonus: It's Ribosomes !!! ;)