Abstract
The structural alignment of proteins has become increasingly important with the growing number of known protein structures. This increase was near exponential in the early 1990s and has become linear over the past several years. We have develop a new algorithm for the comparison of protein structures based on a simple concept：converting protein structure information from 3D level to 1D level in two steps. First step (3D→2D)： is to calculate ramachandran angles (Φ.ψ) from a protein structure coordinates. Second step (2D→1D)：is to translate these ramachandran angles (Φ.ψ) to ramachandran code sequence (each code stands for a distinct area in the ramachandran plot). Launching a well known sequence alignment program such as BLAST to search for similar ramachandran code sequences converted from other proteins and we will get a list of proteins which are similar in structure.