This is a tricky one! Let's think about the logic of the sentence. We're comparing two sets of compounds: the compounds identified by machine-based research (lower quality) and the compounds identified by manual research (more likely to become marketable pharmaceutical products). In the sentence, the second set of compounds (manual research) is referred to by the plural pronoun "those." Since it's THOSE compounds that are more likely to become marketable, it's THOSE compounds that the adjective clause is logically describing, so you're absolutely right, GMATVerbal, that the adjective clause is modifying the pronoun "those."
Now, what about the structure? Remember that a relative pronoun must be as close as possible to the noun OR NOUN IDEA it modifies. A noun idea is a noun and modifier that exist as a unit and cannot be interrupted. In this case, we have the noun idea "those identified by manual research." A relative pronoun immediately following this noun idea could modify EITHER the noun right before it, "research," OR the subject noun of the idea, "those." We need to use logic and agreement to determine the appropriate modification. Here's a similar example:
The cluster of islands, which are constantly at war with one another, is in the Pacific Ocean.
The cluster of islands, which is larger than any other cluster, is in the Pacific Ocean.
Both of these sentences are correct -- the noun idea is "cluster of islands."
Hope that helps!
