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There are many cases where you can verify an answer much more easily than finding it. Not saying that necessarily applies here, but for the more general problem space it isn't the limitation it might appear to be at first.

Protein structures can also be resolved via other methods such as x-ray crystallography of crystallized proteins. Unfortunately, that process can be rather time intensive and isn't viable for all proteins.

Depends on the problem. Factoring into primes seems to be the canonical example.

We would need to know the distribution of incorrect answers. If it didn't give any other answer more than twice then you could trust the 13-time answer to be the correct output of the computation.