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 all the time why MD simulations need an NPT step before production.NPT stands for constant Number of particles, Pressure, and Temperature. And this is one of the most widely used isothermal-isobaric ensembles for MD equilibration. Here is what it does:1-NPT allows the box volume to fluctuate while maintaining constant pressure 2-NPT prevents artificial compression or expansion that would distort the outcome of downstream processes (e.g., binding energy)Please I would highly...

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...