Agent-Supported Protein Structure Similarity Searching

Searching for similar proteins through the comparison of their spatial structures requires efficient and fully automated methods and become an area of dynamic researches in recent years. We developed an algorithm and set of tools called EAST (Energy Alignment Search Tool). The EAST serves as a tool for finding strong protein structural similarities in a database of protein structures. The similarity searching is performed through the comparison and alignment of protein energy profiles received in the computational process based on the molecular mechanics theory. This representation of protein structures reduces the huge search space. In order to accelerate presented method we implemented it with the use of Multi Agent System (MAS). This significantly improved the efficiency of the search process. In the paper, we present the complexity of the search process, the main idea of the EAST algorithm and brief discussion on the advantages of its implementation as MAS.

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