Daniel Kovtun

[Proxima @proximabio]

Join us in Seoul on Tuesday, July 7th for an evening social hosted by @proximabio, @NVIDIAHealth, @DCVC, and @Terray_Tx.

Enjoy an open bar, bites, and a curated group of researchers, founders, and investors at the intersection of AI x Bio.

Spots are limited. RSVP here: https://t.co/gDOMamqkIX

[Proxima @proximabio]

Neo-1: Design and Decode the Structure of Life

[Proxima @proximabio]

Announcing Neo-1: the world’s most advanced atomistic foundation model, unifying structure prediction and all-atom de novo generation for the first time - to decode and design the structure of life 🧵(1/10)

[MLSB (in San Diego + Copenhagen) @workshopmlsb]

Next up we're highlighting the results of the PINDER and PLINDER challenge.

[Proxima @proximabio]

📢 Missed the last lecture? Here's the key takeaways for the upcoming @workshopmlsb challenge: 🧵

📅 The PINDER + PLINDER + MLSB teams are organizing a training workshop Sep 24th - https://t.co/QQsCVJRvZy

🎯 Tasks: flexible protein-protein & protein-ligand docking/co-folding (no holo structures available, only sequences + apo or predicted monomer!)

People will have time to train methods on PINDER/PLINDER splits (no external data!) after MLSB deadline - leaderboard opens Oct 9, closes Nov 9!

To submit to the leaderboard & qualify for the talk, methods will need either a MLSB submission (no acceptance required) or available paper/preprint at leaderboard submission time and provide runnable code with https://t.co/KUmrDdvWGQ & https://t.co/vSCuDFW50H scripts (I/III) 🧵

[Luca Naef @NaefLuca]

🧬 If you love open source, protein structures and are in NYC, don't miss the one and only @bradyajohnston next week! We'll also have Patrick Kunzmann from @biotite_python with us

[Proxima @proximabio]

📢 Join us for an exciting workshop on #MolecularNodes developed & presented by @bradyajohnston on Thu, Aug 1, 11AM-12PM at @vant_ai HQ in NYC.
There will be an opportunity to socialize & ask follow-up questions over snacks afterwards.
Registration: https://t.co/SX905Osjgh

[Gabriele Corso @GabriCorso]

When you hear me rant about the role that industry should have in the field this is exactly what I mean! Incredible team effort led by @vant_ai & @NVIDIA curating new datasets and benchmarks that will provide a ton of value to the field! 🔥🚀

[Janani Durairaj (Jay) @janani_hex]

The bottleneck for a protein-ligand complex (PLI) prediction breakthrough isn't a lack of ML innovation, but accessible data and evaluation to show which ideas work and how to improve them. We (@TorstenSchwede, @vant_ai, @NVIDIA, @MIT_CSAIL) present PLINDER 🧵(1/n)

[Luca Naef @NaefLuca]

💥 Introducing PINDER & PLINDER
With existing evals saturating without clear advances in real life downstream tasks, current progress in AI x Bio is primarily rate-limited by better datasets & evals.
In two back-to-back preprints, we address this via fantastic academic-industry collaborations by @vant_ai @NVIDIA & the group at @TorstenSchwede that co-organizes CASP, @MIT:

Read the release blog posts at:

https://t.co/iMJFERu7Oy & https://t.co/rHdZdOlpZX - 🧵(1/6)

[Luca Naef @NaefLuca]

Huge s/o to @dannykovtun, @janani_hex, @akdelmehmet, @ShinaYusuf_, @agoncear, @ZhonglinJC, @OleinikovasV, @xavier_robin, @clemensisert, @GabriCorso, @hannesstaerk, @emaros96, @akdelmehmet, @zwcarpenter, @mtt_gra, @mmbronstein, @TorstenSchwede and the many more X-less collabrators. This was a huge effort 1.5 years in the making :)

[Mehmet Akdel @AkdelMehmet]

Lots of cool DL tools for PPI complex prediction, but are we evaluating them fairly across practical use-cases? 🤔 We (@vant_ai, @nvidia, @MIT_CSAIL) built PINDER to address this. Can we generalize for novel interfaces, and binding modes, etc.? Let's find out! (1/n)

[Brady Johnston @bradyajohnston]

I have been working like absolute crazy over the past two months for this - #MolecularNodes 4.2 is now released for #b3d 4.2

A huge number of new features - which I will cover some here.

- Selections using @mdanalysis selection language are updated live.

[Luca Naef @NaefLuca]

If you like numpy and protein structures, you'll love @biotite_python! We'll be upstreaming lots of internally useful tools as well

[Biotite @biotite_python]

Biotite 0.41.0 has been released and it brings quite a bunch of improvements: full-fletched SDF file format, reading/writing bonds in @buildmodels NextGen PDBx files and more robust structure superimposition. Read the full changelog at https://t.co/lmERsURrg8. #Bioinformatics

[Proxima @proximabio]

We made it no secret that we love @biotite_python! So much so that Biotite's Patrick Kunzmann has recently joined the team. This is the first of many releases where Patrick is contributing some of the tools he's built at @vant_ai back to Biotite.

[Proxima @proximabio]

We are thrilled to announce a new milestone collaboration with Bristol Myers Squibb (@bmsnews), utilizing our geometric deep learning platform for the rational design of novel molecular glues.

Founder & CEO Zachary Carpenter, and Co-Founder & CTO Luca Naef, sat down with @TheAlexKnapp from Forbes, with commentary from Robert Plenge, Chief Research Officer Bristol Myers Squibb, about why this $674M collaboration marks a paradigm shift for Induced Proximity and drug discovery as a whole.

PR - https://t.co/Mou26DVUwH
Forbes interview - https://t.co/dQ2h7GAbPF

[Proxima @proximabio]

📣 Happening next Friday Jan 19, 2024; 11am ET / 5pm CET / 8am PST!
@generate_biomed 's @ggrigoryanv and @zak_costello's
talk on Chroma at the GenAI series hosted by @mmbronstein and @befcorreia
📄Sign up: https://t.co/bY0d8cTIxJ

[Proxima @proximabio]

Building on success in ongoing projects, we are thrilled to announce the increased scope and range of our partnership with $BPMC bridging the gap between scientific advances in #inducedproximity/targeted protein degradation #TPD and #generativeAI

https://t.co/QJJ4nZePlw

[Proxima @proximabio]

📢 Happening this Friday: Martin Buttenschoen (@Buttenschoen) & Charlie Harris (@charlieharris01) will talk about better benchmarking in small molecule docking and generation!

📅 November 17th, 5 pm CET / 11 am ET / 8 am PT

💥 sign up here https://t.co/cVV3nJiNJO