Protocol Labs

I’m seeing a lot of uninformed takes, like this one, about cell simulation feasibility. I wanted to contribute some facts. Alphafold works for predicting a subset of static structures (not how a protein structure changes shape under forces) on 1) well-ordered regions (not intrinsically disordered regions or long flexible loops) and 2) on proteins with plenty of evolutionary relatives (no orphan proteins). Alphafold solved this subset of static structure prediction with a dataset that took 50 years (PDB; 1971 to ~2020) to collect. It did not solve protein dynamics or how proteins fold into their shapes. Those remain unsolved. Cell simulation is vastly more complex and data hungry than any of this. Exact cell simulation means solving quantum equations for every atom and is totally intractable. But all approximations rely on - and are bottlenecked by - data, not compute. So the extrapolation from “alphafold worked” to “therefore cell simulation is feasible” assumes far too much.