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Representing a given problem as a QUBO problem implies the possibility of running it in a quantum computational environment (generic or specific). The well-known problem of looking for similar functions in biological structures, especially of proteins, is of great interest in the field of Bioinformatics. We give a QUBO formulation for CMO protein problem. Experimental results validate this approach as an alternative to classical methods via combinatorial optimization. For the accomplishment of such experiments, we use the qbsolv tool.

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