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GANDI assembles molecules by joining fragments, which have been previously docked into a protein binding site (henceforth referred to as receptor), with user-defined linker fragments. Heavy atom – hydrogen atom vectors constitute the possible attachment points on both the docked fragments and the linkers. The build-up method implemented in GANDI uses a combination of a genetic algorithm and a random tabu search, where the former is used to select the set of docked fragments and the latter explores possible linker attachments to join the docked fragments.

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