In the paper, we discuss the usage of constant and fuzzy similarity awards while establishing an optimal alignment between energy characteristics of two compared protein energy profiles. Single protein energy profile is a set of energy characteristics of various types of energy. The energy profile is determined for a given protein structure. We use these profiles to find protein molecules of the same structural protein family and inspect conformational modifications in their molecular structures as an effect of biochemical reactions or environmental influences. Energy profiles are received in the computational process based on the molecular mechanics theory. Afterwards, these profiles can be stored in the special purpose database (EDB) and used by the search engine to find similar fragments of protein structures on the energy level. To optimize the alignment path we use modified, energy-adapted Smith-Waterman method with one of the tested similarity awards.

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