Protein folding will not effect the blockchain. hashers will secure the blockchain (confirm in previous post). Hashers will be sharing a portion measured by bench marking hardware of similar value.
If folding is separate from mining, it means that half of the network will effectively run the Folding@home client while the other half will waste their GPU power mining the coin. What the point of the coin, then? Wouldnt it be better just to assign some reward in established cryptocurrency like Bitcoin, mine it and then give rewards to those who contribute to Folding@home? Or at list make your coin merged minable with Bitcoin, like Devcoin and Namecoin had done. Or with LTC if you want scrypt.
In order to make a coin that will do something useful, the
useful algorithm should at the same time ensure the security of the blockchain. So far, this was only done as a proof of concept by Primecoin, because finding prime chains is doubtfully useful. Only this way the hashing power is not a simple waste of energy.
What you so far propose is to waste energy in order to create some doubtful (because the coin will not magically gain value) economic incentive for participating in Folding@home. Does not sound very convincing.