Dorothea Gobbo
@dorotheagb.bsky.social
Computational protein design for therapeutics development | Postdoc at @TromboseLeiden
Reposted by Dorothea Gobbo
Newly-solved protein folding mystery could lead to new ways to design proteins for drug therapeutics, novel biomaterials, and other applications
engineering.yale.edu...
engineering.yale.edu...
A Protein Folding Mystery Solved | News | Yale Engineering
New research reveals protein cores share a 55% packing density, suggesting amino acid jamming controls protein folding with implications for drug design and biomaterials.
engineering.yale.edu
April 19, 2025 at 4:22 PM
Newly-solved protein folding mystery could lead to new ways to design proteins for drug therapeutics, novel biomaterials, and other applications
engineering.yale.edu...
engineering.yale.edu...
Reposted by Dorothea Gobbo
Swinging lever mechanism of myosin shown by time-resolved cryoEM www.nature.com/articles/s41... so glad to finally be able to share this with the community! @astburycentre.bsky.social @astbury-bsl.bsky.social @stemuench.bsky.social @snmcmillan.bsky.social @davidklebl.bsky.social
Swinging lever mechanism of myosin directly shown by time-resolved cryo-EM - Nature
A study using time-resolved cryogenic electron microscopy reveals the swinging lever mechanism of myosin, providing information on the molecular basis behind the production of force and movement by my...
www.nature.com
April 9, 2025 at 5:19 PM
Swinging lever mechanism of myosin shown by time-resolved cryoEM www.nature.com/articles/s41... so glad to finally be able to share this with the community! @astburycentre.bsky.social @astbury-bsl.bsky.social @stemuench.bsky.social @snmcmillan.bsky.social @davidklebl.bsky.social
📌 interesting overview on protein binder design approaches - including antibodies
new blogpost on protein binder design blog.booleanbiotech.com/protein-bind...
Boolean Biotech
blog.booleanbiotech.com
March 9, 2025 at 4:19 PM
📌 interesting overview on protein binder design approaches - including antibodies
Reposted by Dorothea Gobbo
Mature #HIV-1 contains >2000 copies of “spacer peptide 2”, but we didn’t know why. We now see that SP2 binds the matrix protein and triggers the change into its mature arrangement. Summary video from @margotriggi.bsky.social
February 28, 2025 at 2:04 PM
Mature #HIV-1 contains >2000 copies of “spacer peptide 2”, but we didn’t know why. We now see that SP2 binds the matrix protein and triggers the change into its mature arrangement. Summary video from @margotriggi.bsky.social
Exciting news in protein design! On the cover of @science.org is ESM-3, a new AI model that can generate functional protein sequences like a language model. Could this be the next step in AI-driven protein engineering? 🧬✨ #AI #ProteinDesign #ComputationalBiology
Researchers have developed a deep learning protein language model, ESM3, that enables programmable protein design.
Learn more in this week's issue of Science: https://scim.ag/3Qo3HPw
Learn more in this week's issue of Science: https://scim.ag/3Qo3HPw
February 21, 2025 at 6:16 AM
Exciting news in protein design! On the cover of @science.org is ESM-3, a new AI model that can generate functional protein sequences like a language model. Could this be the next step in AI-driven protein engineering? 🧬✨ #AI #ProteinDesign #ComputationalBiology
“Our findings highlight the need for specialised benchmarks for deep learning in protein-ligand interaction prediction. As tasks like co-folding grow more complex, new metrics are needed to assess leakage and difficulty-best defined by interaction similarity, not protein or ligand similarity.”
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 9, 2025 at 9:12 AM
“Our findings highlight the need for specialised benchmarks for deep learning in protein-ligand interaction prediction. As tasks like co-folding grow more complex, new metrics are needed to assess leakage and difficulty-best defined by interaction similarity, not protein or ligand similarity.”
Reposted by Dorothea Gobbo
Foldseek-Multimer is a strategy for complex-to-complex protein structure alignment to quickly perform large-scale structural comparisons between complexes. @martinsteinegger.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 7, 2025 at 3:16 PM
Foldseek-Multimer is a strategy for complex-to-complex protein structure alignment to quickly perform large-scale structural comparisons between complexes. @martinsteinegger.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cool tools by cool people 🚀
AlphaFold2-RAVE: Protein Ensemble Generation with Physics-Based Sampling
Authors: Da Teng, Vanessa J. Meraz, Akashnathan Aranganathan, Xinyu Gu, Pratyush Tiwary
DOI: 10.26434/chemrxiv-2025-q3mwr
Authors: Da Teng, Vanessa J. Meraz, Akashnathan Aranganathan, Xinyu Gu, Pratyush Tiwary
DOI: 10.26434/chemrxiv-2025-q3mwr
February 6, 2025 at 7:03 PM
Cool tools by cool people 🚀
Reposted by Dorothea Gobbo
The human genome encodes potentially thousands of tiny proteins that were previously overlooked. Nature reports on the search to find out what they do. 🧪
‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases
The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do.
go.nature.com
February 2, 2025 at 5:46 PM
The human genome encodes potentially thousands of tiny proteins that were previously overlooked. Nature reports on the search to find out what they do. 🧪