martinpacesa.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Selectively assembling collagen heterotrimers is a challenge. But not for us! Aminopropline-aspartate salt bridges drive the assembly of a hyperstable, a minimal-length, and a special blunt-ended collagen heterotrimer. Now out in @angewandtechemie.bsky.social! onlinelibrary.wiley.com/doi/10.1002/...

submitted 1 day ago • 0 comments

Predicting macromolecular ensembles is incredibly promising. However, as no single experimental method can map a conformational ensemble’s full atomistic landscape, there are foundational questions: What exactly are we trying to predict, and how will we know when we have succeeded?

submitted 4 days ago • 2 comments

A Review from experts in cryo-EM and X-ray crystallography describes the latest and greatest strategies for time-resolved structural biology. www.nature.com/articles/s41...

submitted 5 days ago • 0 comments

While this paper looks interesting, let me just say (again) that (essentially all) NMR ensembles in the PDB are NOT thermodynamic ensembles or meant to represent these. They are "uncertainty ensembles" and using them to benchmark machine learning (or other) models of dynamics is not a good idea.

submitted 6 days ago • 9 comments

Please save-the-date for the #AITHYRA Symposium “AI for Life Science”, which will take place in Vienna at the House of Industry from 8-10 September 2025. Great speakers, interesting framework programme and beautiful location. Registration will open mid May. More info: www.oeaw.ac.at/aithyra/news...

submitted 8 days ago • 0 comments

An interesting post from the other site. These days I read methods comp bio papers w/ wet lab validation while wondering about unreported failures, which is ironic because a data-heavy discipline like comp bio needs the negative data. But comparing it to p-hacking seems totally over-the-top

submitted 7 days ago • 4 comments

Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights: www.nature.com/articles/s41...

submitted 8 days ago • 3 comments

So the tired "preprints shouldn't be cited because they're not peer reviewed" meme is back. Reminder these frequently cited items aren't peer reviewed either: Editorials Books Reviews [some not all] News reports Data Code Websites Social media posts Citations are just links...intent varies 1/2

submitted 9 days ago • 5 comments

I know there are more important things to worry about right now... but it really pisses me off coming across things like this in the literature. Nominally 4.8 Å map... check out Fig S1 😬 (also check out any other #cryoem paper by same group, ~all in BBRC) www.sciencedirect.com/science/arti...

submitted 30 days ago • 5 comments

You’ve heard of vibe coding—meet vibe protein design. Click, launch, and watch the binders roll in. That’s what we're unveiling with @ariaxbio.bsky.social today.

submitted 11 days ago • 2 comments

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1... 🧵🧪

submitted 12 days ago • 2 comments

A Perspective by @stephanieaw.bsky.social and @fraserlab.com discusses ways macromolecules use conformational entropy to control binding, catalysis, and allostery www.nature.com/articles/s41...

submitted 15 days ago • 0 comments

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

submitted 14 days ago • 4 comments

Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM https://www.biorxiv.org/content/10.1101/2025.04.24.650495v1

submitted 15 days ago • 0 comments

We are looking for a postdoctoral fellow to join us to explore telomerase regulation by histones. Please get in touch if this may interest you.

submitted 24 days ago • 0 comments

Hello from Singapore 🇸🇬! Thrilled to be at #ICLR2025 presenting our work on fragment-based drug discovery 🧩. We go beyond virtual screening with a generative, structure-aware approach. 📃 openreview.net/forum?id=bZW...  🔗 github.com/rneeser/Late... A thread 🧵👇

submitted 16 days ago • 2 comments

First post here- Hello Bluesky! Quick science query: These 2D classes are from negative stain of a FLAG pulldown (HEK cell eluate). Does this look like a real complex or a common contaminant? Would live to hear from anyone who’s worked on similar prep! #negativestainEM #pulldown #HEKcells

submitted 19 days ago • 0 comments

After years parked at a Polara, I’m excited to share that my PhD work is finally out! We figured out why imaging at liquid helium temperatures wasn’t working—and how to fix it. 🔗 www.pnas.org/doi/10.1073/...

submitted 17 days ago • 2 comments

By combining high-throughput protein engineering with machine learning, bespoke SpCas9 enzymes are identified that outperform evolution-based and engineered nucleases and base editors in human cells. www.nature.com/articles/s41... #NBTHighlight

submitted 17 days ago • 0 comments

In @nature.com we describe the use of scalable #proteinengineering & #machinelearning to predict millions of bespoke CRISPR enzymes, offering safer & more efficient genome editing tools 🧬🖥️ @rachelsilverstein9.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social www.nature.com/articles/s41...

submitted 18 days ago • 3 comments

Read preprints. Cite preprints. Email people and tell them you loved their preprint. Email people you hated their preprint. Embrace preprints, preprints are good.

submitted 18 days ago • 7 comments

I haven't seen the official announcement but would prefer to see more grants instead. I know it is not under the control of the ERC but I hope the EU manages instead to double the ERC budget. Take money away from the other research initiatives if needed.

submitted 21 days ago • 3 comments

What does pushing the boundaries of model capacity and data scale do for generative protein language models? I’m super excited to share our latest work at Profluent Bio where we begin to explore and test some of our hypotheses! www.biorxiv.org/content/10.1...

submitted 23 days ago • 1 comment

Following Harvard's lead on this, my University's home page now opens on our research contributions to a better world. #GoScienceBears www.berkeley.edu

submitted 24 days ago • 0 comments

Thank you very much for this great analysis!! And for confirming what I have been saying all along, AF3 is comparable at PPI prediction, they just sample more in the original publication

submitted 24 days ago • 1 comment

I am a professor at Columbia University. All of the student NIH training grants have been canceled and now there are reports that ALL funding will be frozen. Why are Universities not banding together and speaking out publicly and forcibly about governmental attacks on biomedical research?

submitted 29 days ago • 56 comments

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

submitted 29 days ago • 3 comments

"potentially replaced by AI-based computational models of toxicity and cell lines and organoid toxicity testing" #whatcouldpossiblygowrong 🤦‍♂️

submitted 29 days ago • 1 comment

"What's the physiological relevance?"

submitted 30 days ago • 7 comments

Good lord

submitted 29 days ago • 0 comments

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 😅

submitted 31 days ago • 5 comments

Amazing talk by Jimi Olaghere sharing his story of receiving the Casgevy treatment and how it improved his life with sickle cell disease ! #CRISPRMED25

submitted 31 days ago • 0 comments

Professional gene editor and professor of Genetics here. The world does not need more negativity. It does not need more nonscientific hype, either. I will be data-based negative and say to Colossal: give me a double-strand break!! [1/3]

submitted 32 days ago • 3 comments

This is the kind of message that makes it all worth it. When someone takes a moment to say thank you, it reminds me why we keep pushing forward—sharing tools, writing posts, and trying to make science more open and accessible. Grateful for the kind words!

submitted 32 days ago • 0 comments

This has been a long journey, but it's now out in final form. @kjamali.bsky.social academic.oup.com/bioinformati...

submitted 32 days ago • 0 comments

Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with @martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org 🧬 Code will be released in a couple weeks

submitted 32 days ago • 5 comments

Another cool paper for understanding the biophysics underlying evolution of TFs.

submitted 33 days ago • 1 comment

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design [new] Protein binder design via model inversion. Distograms optimize structures.

submitted 33 days ago • 0 comments

Woke up to have #BoltzDesign1 on the top of my reading list. Was excited since I heard about it from Sergey in Keystone! Work by @yehlincho.bsky.social et al. www.biorxiv.org/content/10.1...

submitted 33 days ago • 0 comments

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by @yehlincho.bsky.social @martinpacesa.bsky.social @sokrypton.org 🧶🧬 www.biorxiv.org/content/10.1...

submitted 33 days ago • 1 comment

Anyone have slides to share or aware of any public slides on the topic of "introduction to AI in Biology" ? 🙏

submitted 34 days ago • 2 comments

An email I look forward to getting! #BindCraft #ProteinDesign Will have to optimize some settings to get more designs 💻

submitted 46 days ago • 0 comments