Had an informative and enjoyable time at NeurIPS and MLSB. It was great to see my students present their work and catch up with other CPCB students, both past and present.

Excited to be at the first independent @workshopmlsb.bsky.social

If you like to sample from the Boltzmann distribution and are in San Diego for NeurIPS, be sure to check out Rishal's (@rishalchich.bsky.social) poster (#2110). Great work with Nick Boffi (@nmboffi.bsky.social) and Jacky Chen. neurips.cc/virtual/2025... arxiv.org/abs/2507.00846

🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE. Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.

Most of MLIPs dont distinguish between spin states, making them unsuitable for open-shell chemistry. We present AIMNet2-NSE (Neural Spin-charge Equilibration), MLIP that incorporates spin-charge equilibration for systems with arbitrary charge and spin. #compchem #skychem chemrxiv.org/engage/chemr...

Woohoo!

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics? @hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1! 🧵

Nooooooooo.... 😲

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Our new preprint PharmacoForge: Pharmacophore Generation with Diffusion Models is out now! PharmacoForge quickly generates pharmacophores for a given protein pocket that identify key binding features and find useful compounds in a pharmacophore search. Check it out! 🧪 doi.org/10.26434/che...

Was proud and honored to hood Dr. Drew McNutt at the Pitt School of Medicine Diploma Ceremony. Here we are rocking both the blue and gold and tartan colors representing our joint Pitt-CMU CompBio PhD program. Congratulations to Drew and the other @cmupittcompbio.bsky.social graduates!

I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out! 📜 : tinyurl.com/utges-LIGYSI...

Two students in the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology have received honorable mentions from the National Science Foundation’s Graduate Research Fellowship Program. Congratulations to Anamarie Martinez and Emma Flynn! Read more: tinyurl.com/GRFPPitt

We're recruiting a 3-year postdoc for the Novo Nordisk - Oxford Fellowship programme! Develop machine learning approaches for fragment library design and experimental optimisation With @fergusimrie.bsky.social and Charlotte Deane Job advert: shorturl.at/3l47e Further details: shorturl.at/u4UkK

Everything is easy in 2D.. - @franknoe.bsky.social

🚀One week left to register for our Symposium on Open Drug Discovery! Join us in Montreal April 7-8 for an exciting program showcasing how open science and AI are driving drug discovery. Some sessions are already sold out, so register now! Register by April 2nd: conscience.ca/symposium2025

Interested in generative modeling and pharmacophores search for SBDD? Check out our talks at #ACSSpring2025

A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved

Our latest ChemRxiv preprint, "Transferable #MachineLearning Interatomic Potential for Pd-Catalyzed Cross-Coupling Reactions" Collaboration with @nsf-ccas.bsky.social @gabegomes.bsky.social @bobbypaton.bsky.social chemrxiv.org/engage/chemr... #compchem #chemsky

The CACHE #2 preprint is now online: bit.ly/3DyCmHN Active learning and fragment growing delivered confirmed hits. A citizen scientist using the Fold-it gaming interface designed the top compound! Kudos to Sasha and Madhushika @thesgc.bsky.social at the bench. @conscience-network.bsky.social

Andrew McNutt, '24 CPCB graduate, is ready for life's next adventure. Before he begins his career in drug discovery, he's taking a well-deserved break to hike the Appalachian Trail from Georgie to Maine. Read more: tinyurl.com/AndrewMcNutt

Welcome to the Bluesky account for Stand Up for Science 2025! Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide! #scienceforall #sciencenotsilence

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔 ➡️ AlphaBridge will identify the most confident interactions, making your analysis easier! 🌐Try it here: alpha-bridge.eu 👀Read more: www.biorxiv.org/content/10.1...

NIH council meeting (NIDCR)scheduled for today, where our R01 grant (3rd percentile) was supposed to be discussed, was postponed indefinitely as a consequence of Trump's executive order which ordered pausing of all communications from all federal agencies. Not good.

Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...

OPIG is now on Bluesky! Follow us for updates about the group's latest work, web app updates, and more. opig.stats.ox.ac.uk

If you want to learn more about BioEmu, join Sarah Lewis and Michael Gastegger in @hannes-stark.bsky.social ‘s online seminar today. bsky.app/profile/hann...

Rishal’s colab notebook will suggest pharmacophores given a receptor structure that can be directly imported into Pharmit for screening. Check it out!

I wrote up a 2024 Year in Review for @avogadro.cc 🧪⚗️ #opensource #chemsky In short, the community is amazing. Significant translations into 17 languages including 🇭🇷🇫🇷🇭🇺🇰🇷🇷🇴🇪🇸Tamil, 🇺🇦🇨🇳🇬🇪🇩🇪🇯🇵🇵🇹🇧🇷🇷🇸🇹🇷 .. and of course dozens of features and bug fixes discuss.avogadro.cc/t/2024-year-...

These ligands make up 33% of the v2 plinder test set (shown with counts): MG 94 NAG 72 NAG-NAG 64 ZN 44 MN 32 BMP 30 HEM 24 EDO 18 SO4 17 PO4 16 ADP 15 GOL 13 ANP 13 CA 13 FMN 11

Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving. Happy holidays everyone! www.plinder.sh/blog/updates

Boltz v0.4.0 is here! Today, we’re releasing our full data processing pipeline, making it easier than ever to build on top of Boltz. This release also includes our evaluation code and new results. Oh, and also pocket conditioning :)

Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology

Last week several of our students presented their research at NeurIPS 2024 in Vancouver. We are so proud of the excellent work that they've accomplished and shared with the scientific community! 🧪 Check out each of their papers below:

New version of Dockformer preprint landed on arXiv. This virtual screening docking method outperforms all Deep Learning-based approaches, achieving success rates of 90.53% on PDBbind and 82.71% on PoseBusters. Expected to accelerate drug discovery and reduce drug design costs.

With @polarishub.io we’ve built out infrastructure to make hosting and using large scale, ML ready dataset and benchmarks easy. In addition to the dataloaders, we could also maintain leaderboards. Would be happy to explore ways in which we can support the awesome work you’re doing with Plinder.

The American Journal of Human Genetics sat with @fritzroth.bsky.social in the latest "Inside AJHG" to discuss his recently published paper, “A missense variant effect map for the human tumor suppressor protein CHK2.”➡️https://www.ashg.org/ajhg/inside-ajhg-with-fritz-roth/ #ASHG #GeneticsDiscoveries

I'm presenting a new paper "Exploring Discrete Flow Matching for 3D De Novo Molecule Generation" at @workshopmlsb.bsky.social this week! More info in this thread but reach out if want to chat at NeurIPS about generative models or molecular design. arxiv.org/abs/2411.16644

Going into @workshopmlsb.bsky.social , a few thoughts on the PLINDER dataset. This is a monumental and highly appreciated undertaking for extracting protein-ligand interactions from the PDB. First the good...

Concept Bottleneck Language Models For protein design - Introduce CB-pLM (Concept Bottleneck Protein Language Models) from 24M to 3B, trained on UniRef50 and SwissProt over 718 concepts (including Cluster name, Biological process, and Biopython-derived features, etc.) arxiv.org/abs/2411.06090

It’s worth opening the notebook if only to see the cool molecular animations in py3dmol.

FlowMol at your fingertips! We just released a colab notebook to make using FlowMol super easy. Come chat with us tomorrow at @workshopmlsb ! #NeurIPS2024 🧪 colab.research.google.com/github/Dunni...

Early December, the CASP16 Meeting was held in the Palladium resort in Punta Cana, Dominican Republic. Nick Grishin, myself, and Qian Qong presented the assessment of the monomeric structure predictions, the assembly predictions and of monomers in their oligomeric context. 1/n

Excited about BioEmu? Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills aka.ms/ai4science-r...

More excellent work from the indomitable @ian-dunn.bsky.social Come check it out at @workshopmlsb.bsky.social

CACHE3 results are out. We didn’t participate because I didn’t have my act together, but it looks like a win for deep docking. When will nextgen end-to-end DL docking show up/take over in these super important exercises? @conscience-network.bsky.social cache-challenge.org/results-cach...