Today, we’re thrilled to announce two exciting launches, powered by our partnership with @googlecloud: our first protein LLM, AA-0, and our new model API, a powerful tool designed to bring biological AI models directly to machine learning scientists. hubs.la/Q02Q58BM0
A good test for any structure prediction model is its predictive accuracy for novel entrants to the PDB. I just ran Chai-1 on structure 9CBK released yesterday on the PDB (and importantly not yet included in the training set for Chai-1). 🖥️🧬 Chai-1 predicted 9CBK's…
Modelling protein complexes with crosslinking mass spectrometry and deep learning @NatureComms - The study presents AlphaLink, a deep learning approach that integrates crosslinking mass spectrometry (MS) data with AlphaFold-Multimer, significantly improving protein complex…
Introducing PaperQA2, the first AI agent that conducts entire scientific literature reviews on its own. PaperQA2 is also the first agent to beat PhD and Postdoc-level biology researchers on multiple literature research tasks, as measured both by accuracy on objective benchmarks…
Another nice recent papers showing the power of combining MD with diffusion models. This one from @therealpeterobi where they show you can use it to make umbrella sampling more efficient. pubs.acs.org/doi/10.1021/ac…
You know a field is taking off when you regularly see multiple order of magnitude improvements in performance. Thats whats happening in deep learning for molecular simulation. This field is going to be transformed. Latest example: 1/n
Not an ML expert, but want to understand AlphaFold3 (AF3)? I wrote a simple-to-understand AF3 field guide and sprinkled my opinions in along the way. The full essay is linked at the END of the thread. Here's a TL;DR 🧵
AlphaFastPPi: a fast AlphaFold-Multimer-based pipeline for high-throughput screening biorxiv.org/cgi/content/sh… #biorxiv_bioinfo
Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field | Journal of the American Chemical Society @uclachem @ucla #Directed #Evolution #Protoglobin #Electric #Field pubs.acs.org/doi/10.1021/ja…
Has anyone repeated this study, or one like it, for any de novo designed hyperstable proteins (e.g., Baker lab miniproteins)? science.org/doi/10.1126/sc…
Ever wondered if we could model #water to autoionize and correctly predict pH = 7? 🤔 Well, now we can! 😎 In our latest @ChemRxiv preprint, we introduce a #deepneuralnetwork potential trained on density-corrected #DFT that predicts the autoionization constant of water to be Kw…
We investigated AlphaFold3 against RoseTTAfold-AllAtom and a new variant of Metal3D for prediction of metal-protein complexes. Tl;dr AlphaFold3 is as good as specialized tools on metal ion prediction. RFAA not so much. Some interesting findings in below thread: 1/
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