In a recent paper with David Young, and team, we laid the foundations for a framework uncovering novel mechanisms for targeting autoimmune diseases and conditions like sepsis. Here are the three main takeaways: -Analysis of 32 placental mammal FCGR1A sequences revealed two critical binding residues, H148 and W149, as the strongest signatures of evolutionary positive selection, both at the FcγRI-IgG binding interface.-Reconstructed ancestral variants (H148P and W149R) subjected to 100 ns MD...

I recently used BioEmu for some testing. This could be a complement for a regular MD simulations pipeline but don’t believe it will replace MDS entirely. BioEmu’s model pipeline is quite powerful. It combines one pretraining step with two finetuning steps, drawing on experimentally determined structures, over 200 milliseconds of MD simulation data, and protein stability measurements from in vitro testing. That last piece is super important. Incorporating wet lab data significantly improves...

I get asked if AI can design a new protein from scratch. The answer used to be sort of, now it's yes.The most widely used approach is via diffusion modelsThe same underlying approach behind image generators, have been adapted to generate protein backbones from scratch. Tools like RFdiffusion take a structure prediction network and repurpose it as a generative model.Starting from noise, iteratively denoise, and you end up with a novel, physically plausible protein backbone. Then a separate...