Abstract
The similarity measures for molecules play an important role for research in chemistry, biology and drug design. In order to obtain similarity measures for giant molecules such as muscle protein titin, the existing classical algorithms possess high computational complexity and many other disadvantages. An effective quantum algorithm, Quantum Method for Similarity Measures for Molecules (QMSM), is introduced to obtain similarity measure for molecules based on the quantum phase estimation algorithm. Moreover, we discuss the feasibility of simulating the quantum algorithm QMSM with quantum circuits. Finally, the performance evaluation and comparison of the QMSM algorithm are presented, where the QMSM can obtain exponential speedups compared to its classical counterparts.
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