Elena Rogoulenko
@rogoulenko.bsky.social
Ph.D student | Prof. Koby Levy group | Weizmann Institute of Science |
Molecular Dynamics of Biomolecules 🧬
Molecular Dynamics of Biomolecules 🧬
Pinned
Elena Rogoulenko
@rogoulenko.bsky.social
· Nov 13
Skipping events impose repeated binding attempts: profound kinetic implications of protein–DNA conformational changes
Abstract. The kinetics of protein–DNA recognition, along with its thermodynamic properties, including affinity and specificity, play a central role in shap
doi.org
Reposted by Elena Rogoulenko
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
June 3, 2025 at 1:31 AM
🚀 Excited to release BoltzDesign1!
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
✨ Now with LogMD-based trajectory visualization.
🔗 Demo: rcsb.ai/ff9c2b1ee8
Feedback & collabs welcome! 🙌
🔗: GitHub: github.com/yehlincho/Bo...
🔗: Colab: colab.research.google.com/github/yehli...
@sokrypton.org @martinpacesa.bsky.social
Reposted by Elena Rogoulenko
The biggest reason we don't actually have a "replication crisis" is that science is a process of advancing what's working, and not fixing what hasn't. Sometimes it's slow, and we backtrack a bit. But it's never stalled.
That said, the strain on scientific publishing is generating a lot of crap.
That said, the strain on scientific publishing is generating a lot of crap.
May 28, 2025 at 4:18 AM
The biggest reason we don't actually have a "replication crisis" is that science is a process of advancing what's working, and not fixing what hasn't. Sometimes it's slow, and we backtrack a bit. But it's never stalled.
That said, the strain on scientific publishing is generating a lot of crap.
That said, the strain on scientific publishing is generating a lot of crap.
Reposted by Elena Rogoulenko
Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...
GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain types of data visualization - What are they and why are they bad.
Friends don't let friends make certain types of data visualization - What are they and why are they bad. - GitHub - cxli233/FriendsDontLetFriends: Friends don't let friends make certain ty...
github.com
May 25, 2025 at 7:05 AM
Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...
Reposted by Elena Rogoulenko
Reposted by Elena Rogoulenko
🚨Our new paper is online🚨
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
The human proteome with direct physical access to DNA
Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living
cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale
of minutes with single-amino-aci...
www.cell.com
May 22, 2025 at 6:44 PM
🚨Our new paper is online🚨
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
Reposted by Elena Rogoulenko
Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social
🔗 Preprint here tinyurl.com/3a74uanv
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social
🔗 Preprint here tinyurl.com/3a74uanv
April 11, 2025 at 8:35 AM
Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social
🔗 Preprint here tinyurl.com/3a74uanv
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social
🔗 Preprint here tinyurl.com/3a74uanv
Reposted by Elena Rogoulenko
If anyone has any tips for fellowships or grants or giftfunds our group can apply for (in the US), please send our way.
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
April 9, 2025 at 12:30 PM
If anyone has any tips for fellowships or grants or giftfunds our group can apply for (in the US), please send our way.
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅
Reposted by Elena Rogoulenko
Movies as paper titles:
Splinter, M. et al. (1990). "Traditional ninjitsu training increases overall survivability (OS) in an adolescent cohort of wood turtles, Glyptemys insculpta, exposed to ionizing radiation in the New York sewer system." Rept Gen. 90(6):407-409.
Splinter, M. et al. (1990). "Traditional ninjitsu training increases overall survivability (OS) in an adolescent cohort of wood turtles, Glyptemys insculpta, exposed to ionizing radiation in the New York sewer system." Rept Gen. 90(6):407-409.
January 29, 2025 at 4:08 PM
Movies as paper titles:
Splinter, M. et al. (1990). "Traditional ninjitsu training increases overall survivability (OS) in an adolescent cohort of wood turtles, Glyptemys insculpta, exposed to ionizing radiation in the New York sewer system." Rept Gen. 90(6):407-409.
Splinter, M. et al. (1990). "Traditional ninjitsu training increases overall survivability (OS) in an adolescent cohort of wood turtles, Glyptemys insculpta, exposed to ionizing radiation in the New York sewer system." Rept Gen. 90(6):407-409.
Reposted by Elena Rogoulenko
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Structure-guided discovery of viral proteins that inhibit host immunity
Large-scale, structure-guided computational pipeline sifts through millions of phage
proteins to identify those that bind and antagonize host immune proteins. Detected
proteins are shown to inhibit no...
www.cell.com
January 23, 2025 at 4:12 PM
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Reposted by Elena Rogoulenko
The Rey lab at @pasteur.fr is happy to join the BlueSky community.
Please repost and consider adding us to #StructuralBiology and #Virology packs
Please repost and consider adding us to #StructuralBiology and #Virology packs
January 22, 2025 at 8:29 AM
The Rey lab at @pasteur.fr is happy to join the BlueSky community.
Please repost and consider adding us to #StructuralBiology and #Virology packs
Please repost and consider adding us to #StructuralBiology and #Virology packs
Reposted by Elena Rogoulenko
Any recommendations for a membrane dye compatible with HCR/smFISH?
January 22, 2025 at 7:29 AM
Any recommendations for a membrane dye compatible with HCR/smFISH?
Reposted by Elena Rogoulenko
I'm organizing a Keystone symposium, along with Liz Kellogg and @possuhuanglab.bsky.social, on machine learning and macromolecules. Mar 23-26 in Keystone, Colorado. We have a great lineup and deadlines are coming up soon!
Machine Learning Applied to Macromolecular Structure and Function | Keystone Symposia
Join us at the Keystone Symposia on Machine Learning Applied to Macromolecular Structure and Function, March 2025, in Keystone, with field leaders!
www.keystonesymposia.org
January 15, 2025 at 8:47 PM
I'm organizing a Keystone symposium, along with Liz Kellogg and @possuhuanglab.bsky.social, on machine learning and macromolecules. Mar 23-26 in Keystone, Colorado. We have a great lineup and deadlines are coming up soon!
Reposted by Elena Rogoulenko
Over 60 German universities quit social media platform X.
Platform accused of failing to uphold values of diversity, freedom, and scholarship.
Platform accused of failing to uphold values of diversity, freedom, and scholarship.
Over 60 German universities quit social media platform X
Platform accused of failing to uphold values of diversity, freedom, and scholarship - Anadolu Ajansı
www.aa.com.tr
January 12, 2025 at 12:27 PM
Over 60 German universities quit social media platform X.
Platform accused of failing to uphold values of diversity, freedom, and scholarship.
Platform accused of failing to uphold values of diversity, freedom, and scholarship.
Reposted by Elena Rogoulenko
MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures
With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly
www.eurekalert.org/news-release...
With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly
www.eurekalert.org/news-release...
MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures
Researchers in the MIT Jameel Clinic for Machine Learning in Health developed a fully open-source biomolecular structure prediction model that achieves state-of-the-art performance, at the level of Al...
www.eurekalert.org
December 22, 2024 at 5:33 PM
MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures
With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly
www.eurekalert.org/news-release...
With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly
www.eurekalert.org/news-release...
Reposted by Elena Rogoulenko
💥 Reminder: 💥
We are still looking for a postdoc (we actually have enough funds for two!) to work on this promising project.
Details in the ad and the alt text
🧪 🧬 🔬 🐁
#RNASky #RNABiology #Cytoskel #TunnelingNanotubes
We are still looking for a postdoc (we actually have enough funds for two!) to work on this promising project.
Details in the ad and the alt text
🧪 🧬 🔬 🐁
#RNASky #RNABiology #Cytoskel #TunnelingNanotubes
December 17, 2024 at 2:00 PM
💥 Reminder: 💥
We are still looking for a postdoc (we actually have enough funds for two!) to work on this promising project.
Details in the ad and the alt text
🧪 🧬 🔬 🐁
#RNASky #RNABiology #Cytoskel #TunnelingNanotubes
We are still looking for a postdoc (we actually have enough funds for two!) to work on this promising project.
Details in the ad and the alt text
🧪 🧬 🔬 🐁
#RNASky #RNABiology #Cytoskel #TunnelingNanotubes
Reposted by Elena Rogoulenko
MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 21, 2024 at 8:12 AM
MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Elena Rogoulenko
AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics
A novel machine-learning-based force field for protein thermodynamics. It uses an all-heavy-atom approach without hydrogens to simplify simulations while maintaining key dynamics.
pubs.acs.org/doi/10.1021/...
A novel machine-learning-based force field for protein thermodynamics. It uses an all-heavy-atom approach without hydrogens to simplify simulations while maintaining key dynamics.
pubs.acs.org/doi/10.1021/...
November 19, 2024 at 3:16 PM
AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics
A novel machine-learning-based force field for protein thermodynamics. It uses an all-heavy-atom approach without hydrogens to simplify simulations while maintaining key dynamics.
pubs.acs.org/doi/10.1021/...
A novel machine-learning-based force field for protein thermodynamics. It uses an all-heavy-atom approach without hydrogens to simplify simulations while maintaining key dynamics.
pubs.acs.org/doi/10.1021/...
Hey, @bsky.app, @support.bsky.team how about a #CatchThemAll tab in the profile listing all the starter packs the profile is a part of?
November 15, 2024 at 6:45 AM
Hey, @bsky.app, @support.bsky.team how about a #CatchThemAll tab in the profile listing all the starter packs the profile is a part of?
Reposted by Elena Rogoulenko
Looks like Bryan Dickinson isn’t here yet so I’m cross posting his challenge:
“if you or someone you know thinks they can actually predict PPIs, prove it. Here is a link to our blinded protein sequence data”
dickinsonlab.uchicago.edu/ppi-challenge
“if you or someone you know thinks they can actually predict PPIs, prove it. Here is a link to our blinded protein sequence data”
dickinsonlab.uchicago.edu/ppi-challenge
PPI Challenge | dickinson-group
dickinsonlab.uchicago.edu
November 14, 2024 at 12:01 AM
Looks like Bryan Dickinson isn’t here yet so I’m cross posting his challenge:
“if you or someone you know thinks they can actually predict PPIs, prove it. Here is a link to our blinded protein sequence data”
dickinsonlab.uchicago.edu/ppi-challenge
“if you or someone you know thinks they can actually predict PPIs, prove it. Here is a link to our blinded protein sequence data”
dickinsonlab.uchicago.edu/ppi-challenge
Reposted by Elena Rogoulenko
Hi Bluesky! I made a 3D chromatin starter pack.
Let me know if you would like to be added.
go.bsky.app/6tTQdqQ
Let me know if you would like to be added.
go.bsky.app/6tTQdqQ
November 13, 2024 at 5:55 PM
Hi Bluesky! I made a 3D chromatin starter pack.
Let me know if you would like to be added.
go.bsky.app/6tTQdqQ
Let me know if you would like to be added.
go.bsky.app/6tTQdqQ
Check out my paper with @koby_group on how proteins can get fooled by DNA conformational changes and miss their binding site, published in @NAR_open
#DNA #Proteins #compbio
#DNA #Proteins #compbio
Skipping events impose repeated binding attempts: profound kinetic implications of protein–DNA conformational changes
Abstract. The kinetics of protein–DNA recognition, along with its thermodynamic properties, including affinity and specificity, play a central role in shap
doi.org
November 13, 2024 at 5:10 AM