1. A method of finding 3D similarities in protein the structure of a first molecule and of a second molecule, comprising the steps of: processing preselected structure information of alignment of residue-residue correspondence, comparing the first molecule and the second molecule using said preselected information and using Longest Continuous Segments (LCS) analysis, comparing the first molecule and the second molecule using said preselected information and using Global Distance Test (GDT) analysis, comparing the first molecule and the second molecule using said preselected information and using Local Global Alignment Scoring function (LGA_S) analysis, repeating said steps to find all the regions of 3D similarities between considered protein structures, and generating an output containing complete information about the quality of the calculated alignment.