Eva Smorodina
@evasmorodina.bsky.social
Computational structural biologist
Reposted by Eva Smorodina
Clustering hundreds of millions of molecules in a single workstation is now a possibility!
Check the new code: github.com/mqcomplab/bb...
Check the new code: github.com/mqcomplab/bb...
GitHub - mqcomplab/bblean
Contribute to mqcomplab/bblean development by creating an account on GitHub.
github.com
September 16, 2025 at 5:11 PM
Clustering hundreds of millions of molecules in a single workstation is now a possibility!
Check the new code: github.com/mqcomplab/bb...
Check the new code: github.com/mqcomplab/bb...
Reposted by Eva Smorodina
Reposted by Eva Smorodina
A compelling review of how ML/AI could help in the quest to find an enzyme for every reaction.
@jsunn-y.bsky.social @francescazfl.bsky.social Yueming Long @francesarnold.bsky.social
www.cell.com/cell-systems...
@jsunn-y.bsky.social @francescazfl.bsky.social Yueming Long @francesarnold.bsky.social
www.cell.com/cell-systems...
September 3, 2025 at 12:47 PM
A compelling review of how ML/AI could help in the quest to find an enzyme for every reaction.
@jsunn-y.bsky.social @francescazfl.bsky.social Yueming Long @francesarnold.bsky.social
www.cell.com/cell-systems...
@jsunn-y.bsky.social @francescazfl.bsky.social Yueming Long @francesarnold.bsky.social
www.cell.com/cell-systems...
Reposted by Eva Smorodina
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 10:48 AM
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Reposted by Eva Smorodina
Glad to share the final version of our story about the UBR4 complex, an E4 ligase protein quality control hub @science.org. Now with more cryo-EM structures and a deeper dive into substrate recognition, especially escaped mitochondrial proteins @clausenlab.bsky.social www.science.org/doi/10.1126/...
August 28, 2025 at 6:54 PM
Glad to share the final version of our story about the UBR4 complex, an E4 ligase protein quality control hub @science.org. Now with more cryo-EM structures and a deeper dive into substrate recognition, especially escaped mitochondrial proteins @clausenlab.bsky.social www.science.org/doi/10.1126/...
Reposted by Eva Smorodina
#CCPBioSim will be running their annual training week of hands-on workshops in basic biomolecular simulation techniques from the 13th-17th October, in Sheffield.
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
August 29, 2025 at 7:46 AM
#CCPBioSim will be running their annual training week of hands-on workshops in basic biomolecular simulation techniques from the 13th-17th October, in Sheffield.
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
For more details, visit www.ccpbiosim.ac.uk/training2025
The registration link there will open shortly! #compchem
Reposted by Eva Smorodina
New degrader paper using the immunoproteasome. Congrats Cody Loy and Tim Harris!
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Degradation of Abl Utilizing an Immunoproteasome N-Degron Prodrug
Targeted protein degradation is an emerging therapeutic strategy that leverages the cell’s natural protein clearance pathways to eliminate proteins of interest (POIs). One common approach involves bif...
pubs.acs.org
August 20, 2025 at 4:53 PM
New degrader paper using the immunoproteasome. Congrats Cody Loy and Tim Harris!
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Reposted by Eva Smorodina
encapsulate your target proteins for cryoEM structural determination within highly hydrophilic, structurally homogeneous, and stable protein shells 🤩
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
August 22, 2025 at 10:04 PM
encapsulate your target proteins for cryoEM structural determination within highly hydrophilic, structurally homogeneous, and stable protein shells 🤩
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Eva Smorodina
We're excited to present our latest article in Nature Machine Intelligence - Boosting the predictive power of protein representations with a corpus of text annotations.
Link: www.nature.com/articles/s42...
[1/4]
Link: www.nature.com/articles/s42...
[1/4]
August 21, 2025 at 7:34 PM
We're excited to present our latest article in Nature Machine Intelligence - Boosting the predictive power of protein representations with a corpus of text annotations.
Link: www.nature.com/articles/s42...
[1/4]
Link: www.nature.com/articles/s42...
[1/4]
Reposted by Eva Smorodina
CACHE 7 is launched with support from the @gatesfoundation.bsky.social and unpublished data from Damian Young at @bcmhouston.bsky.social, Tim Willson @thesgc.bsky.social and Neelagandan Kamaria InSTEM. Design selective PGK2 inhibitors. We'll test them experimentally.
bit.ly/4lnVYOs
bit.ly/4lnVYOs
August 12, 2025 at 7:07 PM
CACHE 7 is launched with support from the @gatesfoundation.bsky.social and unpublished data from Damian Young at @bcmhouston.bsky.social, Tim Willson @thesgc.bsky.social and Neelagandan Kamaria InSTEM. Design selective PGK2 inhibitors. We'll test them experimentally.
bit.ly/4lnVYOs
bit.ly/4lnVYOs
Reposted by Eva Smorodina
📢 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 Eva Smorodina
🚀 My first Cryo-EM structures are OUT on the PDB!
🎉Super excited about this milestone as PhD, it’s been a journey, and I’m grateful to finally have these as my first Cryo-EM structures! 🙌
🔁Thank you for sharing!❤️
Read @daaninthelab.bsky.social et. al.: www.science.org/doi/10.1126/...
⬇️ 2nd video
🎉Super excited about this milestone as PhD, it’s been a journey, and I’m grateful to finally have these as my first Cryo-EM structures! 🙌
🔁Thank you for sharing!❤️
Read @daaninthelab.bsky.social et. al.: www.science.org/doi/10.1126/...
⬇️ 2nd video
July 9, 2025 at 10:43 PM
🚀 My first Cryo-EM structures are OUT on the PDB!
🎉Super excited about this milestone as PhD, it’s been a journey, and I’m grateful to finally have these as my first Cryo-EM structures! 🙌
🔁Thank you for sharing!❤️
Read @daaninthelab.bsky.social et. al.: www.science.org/doi/10.1126/...
⬇️ 2nd video
🎉Super excited about this milestone as PhD, it’s been a journey, and I’m grateful to finally have these as my first Cryo-EM structures! 🙌
🔁Thank you for sharing!❤️
Read @daaninthelab.bsky.social et. al.: www.science.org/doi/10.1126/...
⬇️ 2nd video
Reposted by Eva Smorodina
🚨It’s out @embojournal.org 🚨
Cardiolipin inhibits Caspase-4/11!
Huge thanks to my brilliant supervisors Kate & Pablo, to @s-burgener.bsky.social & Mercedes and all the @inflammasomelab.bsky.social, it was a joy working and laughing with you, and to @brozlab.bsky.social & Si Ming lab.
Cardiolipin inhibits Caspase-4/11!
Huge thanks to my brilliant supervisors Kate & Pablo, to @s-burgener.bsky.social & Mercedes and all the @inflammasomelab.bsky.social, it was a joy working and laughing with you, and to @brozlab.bsky.social & Si Ming lab.
July 23, 2025 at 11:23 AM
🚨It’s out @embojournal.org 🚨
Cardiolipin inhibits Caspase-4/11!
Huge thanks to my brilliant supervisors Kate & Pablo, to @s-burgener.bsky.social & Mercedes and all the @inflammasomelab.bsky.social, it was a joy working and laughing with you, and to @brozlab.bsky.social & Si Ming lab.
Cardiolipin inhibits Caspase-4/11!
Huge thanks to my brilliant supervisors Kate & Pablo, to @s-burgener.bsky.social & Mercedes and all the @inflammasomelab.bsky.social, it was a joy working and laughing with you, and to @brozlab.bsky.social & Si Ming lab.
Reposted by Eva Smorodina
We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation.
August 19, 2025 at 5:16 PM
We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation.
Reposted by Eva Smorodina
Switching next to protein protein interactions, we used arguably my favorite protein A34F GB1 to demonstrate that these glycopolymers stabilize protein protein interactions in a similar fashion to protein folding, via chemical interactions.
August 13, 2025 at 5:25 PM
Switching next to protein protein interactions, we used arguably my favorite protein A34F GB1 to demonstrate that these glycopolymers stabilize protein protein interactions in a similar fashion to protein folding, via chemical interactions.
Reposted by Eva Smorodina
Interested in solvation free energies of small molecules and proteins?
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
August 14, 2025 at 4:45 PM
Interested in solvation free energies of small molecules and proteins?
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST):
doi.org/10.33011/liv...
#compchem
Reposted by Eva Smorodina
Pushing down to the structures of ever-smaller proteins (and ever-smaller crystals!)
The Frontiers of Structure
www.science.org
August 13, 2025 at 9:43 PM
Pushing down to the structures of ever-smaller proteins (and ever-smaller crystals!)
Reposted by Eva Smorodina
Happy to share the latest from the lab, led by Daniel Alvarez, in collaboration with @lizconibear.bsky.social. In this AA-MD tour-de-force, we delve deep into the mechanism and energetics of lipid uptake by bridge-like lipid transfer proteins, and we learn a few interesting things along the way...
August 7, 2025 at 8:45 AM
Happy to share the latest from the lab, led by Daniel Alvarez, in collaboration with @lizconibear.bsky.social. In this AA-MD tour-de-force, we delve deep into the mechanism and energetics of lipid uptake by bridge-like lipid transfer proteins, and we learn a few interesting things along the way...
Reposted by Eva Smorodina
Thrilled to share my first corresponding author paper as a project leader in @hillerlab.bsky.social Amazing work from first author @annaleder.bsky.social We discovered multi-chaperone condensates in the ER that revolutionise the current vision of protein folding!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 11, 2025 at 10:14 AM
Thrilled to share my first corresponding author paper as a project leader in @hillerlab.bsky.social Amazing work from first author @annaleder.bsky.social We discovered multi-chaperone condensates in the ER that revolutionise the current vision of protein folding!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Eva Smorodina
Our latest Best Practices article "Developing Monte Carlo Methodologies in Molecular Simulations" is out now and describes how to derive acceptance probabilities for a variety of Monte Carlo moves:
doi.org/10.33011/liv...
#compchem
doi.org/10.33011/liv...
#compchem
August 11, 2025 at 6:32 PM
Our latest Best Practices article "Developing Monte Carlo Methodologies in Molecular Simulations" is out now and describes how to derive acceptance probabilities for a variety of Monte Carlo moves:
doi.org/10.33011/liv...
#compchem
doi.org/10.33011/liv...
#compchem
Reposted by Eva Smorodina
A benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies shows that:
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures
@grocklin.bsky.social
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures
@grocklin.bsky.social
August 8, 2025 at 8:10 PM
A benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies shows that:
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures
@grocklin.bsky.social
- deep learning structural metrics only weakly predict success
- The score distribution is different for different types of structures
@grocklin.bsky.social
Reposted by Eva Smorodina
Physics-based design of efficient Kemp eliminases
@lynnkamerlin.bsky.social
www.nature.com/articles/s41...
@lynnkamerlin.bsky.social
www.nature.com/articles/s41...
June 19, 2025 at 9:18 PM
Physics-based design of efficient Kemp eliminases
@lynnkamerlin.bsky.social
www.nature.com/articles/s41...
@lynnkamerlin.bsky.social
www.nature.com/articles/s41...
Reposted by Eva Smorodina
June 25, 2025 at 2:19 PM
Reposted by Eva Smorodina
Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!
July 19, 2025 at 8:46 PM
Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!
Reposted by Eva Smorodina
Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/...
Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules
The conformational ensemble of a molecule is strongly influenced by the surrounding environment. Correctly modeling the effect of any given environment is, hence, of pivotal importance in computationa...
pubs.acs.org
August 4, 2025 at 1:20 PM
Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/...