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Sure, I get the mechanics. My question is, if we can incorporate knowledge about chaperones into the models as explicit or latent variables, so to speak, then why can’t the models predict something like “probability of molecule a given the presence of chaperone b”?

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it sure can, given enough computation, chaperones are often protiens themselves but can be otherwise; they are subject to the same forces so twist and turn fold and conform.

they often interact with each other, and must exert influence at proper stage of modification.

other effects beyond foldingoccur, such as addition or elimination of prosthetic groups.

the take home message is fallacy of oversimplifying the process of many molecules plus ionic enironment, interacting to influence a single molecule

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