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

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.

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...

Just a nice reminder! 🧪🧬🖥️ I found this GitHub very useful: github.com/cxli233/Frie...

OpenAI just updated ChatGPT to be able to use RDKit, a cheminformatics Python package.

OpenAI's president says this makes ChatGPT "useful for scientific work across health, biology, and chemistry," but it is hilariously still not good at chemistry (🧵)

#chemsky #AI ⚗️🧪🖥️

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...

🚨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...

I was starting to think I was the only one having this self-forwarding glitch 😆. @bsky.app really needs to sort it out.

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

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 😅

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.

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...

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...

The Rey lab at @pasteur.fr is happy to join the BlueSky community.
Please repost and consider adding us to #StructuralBiology and #Virology packs

Any recommendations for a membrane dye compatible with HCR/smFISH?

The strain on scientific publishing Abstract. Scientists are increasingly overwhelmed by the volume of articles being published. The total number of articles indexed in Scopus and Web of Science has grown exponentially in recent years; ...

The growth in the number of articles outpaces the growth of the scientific community. Changing policies might address the issue, but can it really make an impact?
Is it possible we’re reaching a critical point and a revolution in scientific publishing practices?

direct.mit.edu/qss/article/...

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!

Over 60 German universities quit social media platform X Platform accused of failing to uphold values of diversity, freedom, and scholarship - Anadolu Ajansı

Over 60 German universities quit social media platform X.

Platform accused of failing to uphold values of diversity, freedom, and scholarship.

Do you remember rewinding the tape with a pen? I truly miss how physical the art was, and how hard we had to work sometimes to get access to it. Really made you appreciate things more.

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...

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...

Post-doctoral Positions Wanted: Talented applicants to study intercellular mRNA trafficking in vitro and in vivo and its application in RNA therapeutics Relevant works: Haimovich et al. 2017 PNAS http://www.pnas.org/content/114/46/E9873.full Dasgupta et al. 2023 eLife https://elifesciences.org/articles/83584 Haimovich et al. 2024 bioRxiv https://www.biorxiv.org/content/10.1101/2024.11.06.622258v1 Contact: Prof. Jeffrey Gerst Dept. of Molecular Genetics jeffrey.gerst@weizmann.ac.il www.weizmann.ac.il/molgen/Gerst/

💥 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

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...

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/...

Although reweighted ABSINTH was calibrated based on experimental data, it was not the approach I had in mind.
I believe this manuscript is the perfect answer for my question, thank you!
(and thanks for joining in)

Thank you for the detailed answer!
Do you think that the data from your experimental setup can be directly used to train DNNs, similar to @alexholehouse.bsky.social ALBATROSS, or @lindorfflarsen.bsky.social CALVADOS (which were trained on experimental data but through CG simulations)?

🙋‍♀️

Very interesting paper!
Do you think using only one peptide and mutating it incrementally can suggest additional size-sequence dependencies?

I almost exclusively use ChimeraX, which gives me the FOMO on not figuring out #MolecularNodes

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?

This is fascinating! It seems that NovumRNA might not only function as a standalone tool for designing treatments but could also be valuable for understanding why certain treatments may have been ineffective. Could it potentially be integrated into standard analysis protocols in drug testing?

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

Hi Bluesky! I made a 3D chromatin starter pack.
Let me know if you would like to be added.
go.bsky.app/6tTQdqQ

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

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