Yes, insurance companies really did cancel fire insurance for Californians 2 months before the LA fires. www.youtube.com/watch?v=5h1H...

Did you know that court docs for name and gender changes are not confidential? You can google a trans person’s current name and find their old, dead name — and vice versa. In CA, my amazing bud Hazel is working to fix this, and she may just be successful. My latest for @sfchronicle.com Gift Link 🎁

Pretty amazing that nonprofit Watch Duty -- which says it has 150 volunteers working around the clock to track wildfires -- has become the most trusted source of information on LA fires. Operated by retired/volunteer firefighters, dispatchers, and reporters. Real people. www.watchduty.org

If you’re in LA, stay safe, leave if you’re told to. Sending good vibes.

As if anyone had any doubt. home.treasury.gov/news/press-r...

Okay…density matrices/operators I can do.

So, DFT is pretty interesting 💀

Well ARC-AGI was cracked by OpenAI with "o3" arcprize.org/blog/oai-o3-...

If people find MSA subsampling useful, they will likely find MDGen very useful and they will definitely find BioEmu useful.

Just nerding out over AI4Biochem with @nathanlabenz.bsky.social www.youtube.com/watch?v=enNr...

UCLA Chem & Biochem is looking for an assistant professor who has "outstanding potential as a scientist, educator, & mentor to students from groups under-represented in the physical sciences". This is part of a cluster hire in physical sciences. @chemjobber.bsky.social recruit.apo.ucla.edu/JPF10039

Immunotherapy for oncology New more effective & cheap anti-venoms Allosteric switch proteins New Alzheimer’s treatments De novo functional nanopores Vaccines And so much more from Baker Lab. Thank you for being such an inspiration and for forging a path forward. 🚀💜 www.youtube.com/live/HnT1VWz...

Thanks! Also check our update to CDR clustering where we modified the D score as max over all dihedral distances including omega, instead of average. Also electron density cutoff to detect peptide flips. Eliminated lots of small CDR clusters with poor density. www.biorxiv.org/content/10.1...

Anthropic needs to get on fine tuning Claude with tree of thought reasoning and GFlowNets.

My apologies to those in love with classical molecular dynamics 😅

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

When my daughter came out to me, she asked if being gay was “natural.” A classmate suggested otherwise… As a professor of animal behavior, I shared 2k+ examples from the animal kingdom! Those became a book, & today it’s still #1 top release and #3 best seller. #LoveWins #WildPride ❤️🏳️‍🌈 a.co/d/947x66x

Improving structure prediction by padding MSAs with synthetic sequences. Potts model-designed seqs worsen prediction performance, so some higher-order coevolutionary interactions appear to be contributing to this boost openreview.net/pdf/fd516f23...

More evidence that protein folding NNs have learned a crude approximation of an energy function, though the authors here suggest it is at the local level exclusively, because it is only able to make incremental refinements in the absence of coevolutionary data academic.oup.com/bioinformati...

Trying to get Baker Lab's new beta-pairing binder design technique going. Not quite there, but I'm getting close. Anyone have good adj and ss .pt prep code, or a bash script to run the model with on said .pt files?

I like collecting good ideas 😁 there are quite a few floating around in AI4Biochem these days. I love piecing together what has been done in the past 6 months and seeing what is possible in the next 6 months. It just gives me so much hope and excitement to be able to look into the near future. 🚀

This looks interesting. Reminds me of this… www.biorxiv.org/content/10.1...

This is a fantastic, bleeding-edge overview of the field. Semi-relatedly, anyone know what happened with AI2BMD? 10k atoms(!), "ab initio accuracy", published in Nature... It sounds great, but very few hits / github stars so I assume few people are using it.

🤔 will need to really look at this dataset. Previously there weren’t any good datasets for this. github.com/Huatsing-Lau...

Who will be at NeurIPS and wants to meet? :) (generative models for biomolecules, ...) Also, in the Wednesday poster session, Bowen Jing and I will present our "Generative Modeling of Molecular Dynamics Trajectories" arxiv.org/abs/2409.178...

New blogpost: The ABCs of Alphafold 3, Boltz and Chai-1 blog.booleanbiotech.com/alphafold3-b...

Nice blogpost by @btnaughton.bsky.social about playing around with the different biomolecular structure prediction models AF3, Boltz-1, and Chai-1! My perspective? Current models are good, but future ones will be much better: let's build them together! 🚀

Design of high specificity binders for peptide-MHC-I complexes www.biorxiv.org/content/10.1... New from the Baker lab

If someone in the community is experienced with this, help is always super welcomed!

Testing out the new Boltz-1 chunking on a hemichannel…if it works, full gap junction is next. I’ll report back with results soon 😊

Pretraining PLMs with both the standard MLM loss and a growth temperature loss dramatically improves prediction of thermostability, as well as identification of thermostabilizing point mutants. Lots of wet lab evaluation www.science.org/doi/10.1126/...

More playing around with Chai-1 & Boltz-1

So pretty! (Chai-1 vs. Boltz-1)

🧠 ^^This^^ is the moat…it’s not your model, it’s your ability to wield it and to pursuade it to conspire with other models to solve a problem.

Oh?! Really?! What an interesting development…I still like Boltz-1, but maybe if I get to know Chai-1 a little I’ll like it too.

Something tells me trying to disrupt/modulate complicated pathways to inhibit cancer is a bit like using mechanist interpretability (ex. Golden Gate Claude) to get neural nets to do something in particular. It can be done, and sometimes must, but top down training of the system is much better.

Thanks Carl for highlighting

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

An RFdiffusion-generated binder conjugated to a single-chain antibody shows antitumor activity in mouse models www.biorxiv.org/content/10.1...