1. A method for searching, among a plurality of target protein data saved in a protein database, a similar protein data that is structurally similar to an inquiry protein data inputted from the outside, comprising the steps of: a) respectively coding three-dimensional relative directional angles (3D RDAs) of the target protein data, and coding a 3D RDA of the inquiry protein data, wherein the coding comprises transforming three-dimensional coordinates of the target protein data into spherical coordinates of the target protein data; b) respectively obtaining a Fourier coefficient of each of the plurality of target protein data by Fourier transforming 3D RDA coding values of the target protein data, and obtaining a Fourier coefficient of the inquiry protein data by Fourier transforming a 3D RDA coding value of the inquiry protein data, wherein the transforming comprises transforming the spherical coordinates obtained in the step a); c) comparing the Fourier coefficients of the target protein data with the Fourier coefficient of the inquiry protein data; and d) outputting the target protein data in structurally similar order in regard to the inquiry protein data based on result of the comparison, and searching the similar protein data among the target protein data outputted in structurally similar order, wherein the steps a), b), c) and d) are performed by a sufficiently programmed computer.