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 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...