Abstract — Analysis of conformational changes is one of the keys to the understanding of protein functions and interactions. For the analysis, we often compare two protein structures, taking flexible regions like hinge regions into consideration. The RMSD (Root Mean Square Deviation) is the most popular measure for comparing two protein structures, but it is only for rigid structures without hinge regions. In this paper, we propose a new measure called RMSDh (Root Mean Square Deviation considering hinges) and its variant RMSDh (k) for comparing two flexible proteins with hinge regions. We also propose novel efficient algorithms for computing them, which can detect the hinge positions at the same time. The RMSDh is suitable for cases where there is one small hinge region in each of the