An Efficient 3D-model In The Application Of The Visualization Of Proteins

The research of the structure of protein has become an important topic in bioinformatics. As a powerful tool, computer is playing more and more important role in this field. It's no doubt that if the 3D-structure of the protein can be presented before the researcher and some assistant functions are offered, that must contribute to the work of the researchers. HJMV (HUST Java Molecular Viewer) is one part of the program of Secondary Database of Protein related with Selenium - the National High Technology Research and Development Program of China (863 Program). The main goal of our research is to offer a method, which let the user can view the 3D-sturcure of the protein directly through the WEB. What's more it provides some assistant functions. HJMV is implemented in Java3D, and through Applet, it meets our goals. But because the pitfalls in performance of Java, like many other visualization tool, the beginning version of HJMV can't load and render the molecule, which is too large. So we consider mainly make some improvement in two aspects-the input module and the render module. HJMV present the data structure of the molecule in tree model. And based on some chemical roles, HJMV optimizes the algorithm for computing the location of the bonds in the molecules. To improve the rendering speed, HJMV offers different approaches of the scene graph for the different scene model, such as stick model, VDW model, tube model, etc. By these methods, HJMV reduces the number of objects created in the program, and especially pay much attention on reusing the 3D object that have the same appearance. For example, HJMV defines the class for the sphere itself, which includes the location information for the molecule. Through the data of the experiment, HJMV has a much better performance then other visualization tools based on Java, such as JMVS, FPV, etc. HJMV can load much larger molecule and have a much better performance in the operations of it. Now the largest molecule HJMV can read is 1GQ2, which includes 67729 atoms, and it also has a much quicker speed in the rendering of the structure of molecules.