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Impractical Joke only stops damage from being prevented by effects that specifically use the word "prevent."

You don't have to choose a target for Impractical Joke. However, if you do and the target is illegal as Impractical Joke tries to resolve, it won't resolve and none of its effects will happen. Damage can still be prevented this turn.

Protection prevents damage, so protection abilities will be unable to prevent damage during a turn in which Impractical Joke has resolved. However, this won't allow spells or abilities to target permanents they wouldn't ordinarily be able to target because of protection, even if that spell or ability would deal damage to those permanents.