| Protein structure analysis is one of the most important topics in the field of life science. The main idea is disposing target protein with X-ray or other physical methods, obtaining the electron density map from the results, and then using the map to achieve the building work to complete the analysis of protein.There are many classical algorithms in the field of protein structure analysis, such as ACMI, TEXTAL and so on. These classical algorithms can build a molecule structure well when the electron density map with high resolution. But when the resolution reduces to 3.0A, the result is not ideal. So we propose a method to build the structure by separating electron density map into blocks and using the symmetry of protein molecules.The research of this paper is divided into three parts. First, we use Phenix to divide a sphere with the radius of 30A in the molecule, and then locate the protein molecules and get the conversion relationship between individual molecules, including rotation matrix and displacement vector. And then we use electron density map blocks and molecular symmetry to mark the connected regions in the molecule and outline the range near the center of each molecule by searching the local area within the radius of 30A. Finally, we segment the protein sequence, get long fragments, locate the fragment in the range using fast rotation algorithm, and split joint them, so as to realize the analysis of protein structure.Finally, we test 4ymx and 3x21 protein molecules. For 4ymx, we extract the electron density map containing two molecules with 2.0A,2.5A and 3.0A resolution. For 3x21 we extract the map containing five molecules with 3.0A resolution. Analyzing the result, we find that our method can outline the range of protein, locate the fragment and build the molecular structure well when the resolution of the electron density map is 3.0A. In the contrast experiment, we combine the method with SAPTF algorithm, and compare it with traditional SAPTF algorithm, we find that the new method has better performance. |
