Although many 3D structures have been solved for proteins to date, functions of some proteins remain unknown. To predict protein functions, comparison of local structures of proteins with pre-defined model structures, whose functions have been elucidated, is widely performed. For the comparison, the root mean square deviation (RMSD) has been used as a conventional index. In this work, adaptive deviation was incorporated, along with Bregmann Divergence Regularized Machine, in order to detect analogous local structures with such model structures more effectively than the conventional index.