Interactive Molecular Visualization Platform For Drug Design

As the main vehicle for biological function, protein, whose function mainly depends onits conformation and spatial structure. While, the protein data which is provided to researchersis generally abstract, thus, it is difficult to know its spatial structure from these data, but itdoes play a crucial role in the research of biology, especially in the observation of thethree-dimensional structure of protein molecules. With the rapid increase of computer science,bioinformatics and biological databases are continuously developing, three-dimensionalvisualization of biological molecules play a principle role in the research of bioinformatics.Interactive molecular visualization platform for drug design can read standard PDB file ofprotein and then finish the task that contains the analysis, screening, processing to obtainuseful information. And what’s more, we use the visualization technology to display thethree-dimensional model of proteins to the user, and provide users multiple observation modelvia molecular visualization platform.Firstly, we finish the original data processing and analysis which are obtained fromprotein molecules, and the data that has been processed is stored in a particular file format inthe PDB. By reading the information from PDB of the spatial structure of the proteinmolecules, then the platform utilizes this information to accomplish geometric modeling,drawing, rendering and projecting three-dimensional models of molecules on the screen.While for the motion model of the protein molecule, we achieve the three-dimensionalinteraction requirements include translation, rotation, scaling and so on. The molecularinteractive visualization platform which is designed for drugs runs for local launch.Secondly, we introduce the protein molecule geometry and motion models in this paperand propose the specific implement method based on the two models. Geometric model of theprotein molecule that is also named three-dimensional structure of protein molecules,establishes the reasonable models of protein molecules stick model, Sphere model, Cartoonmodels on the basis of molecular modeling, We emphasis on the modeling approach of Cartoon model of β-sheet model. After processing the raw data, we use the method of Beziercurves and the difference fitting method of least squares fitting the corresponding point of thenormal to draw β-sheet model. The protein motion-model means the part of interaction withthe user, which uses a trackball (Track Ball) technology to convert the two-dimensionalmotion of mouse into three-dimensional structures on screen.Finally, interactive molecular visualization platform for drug design is achieved byOpenGL, OpenGL Shading Language(GLSL) and C++technology. We succeed in displayinga variety of three-dimensional structure of protein molecules, and meanwhile we realize the athree-dimensional interactive operation between platform and users. The platform utilizeGLSL technique to draw a three-dimensional structure of molecules, separating the traditionalOpenGL vertex transformation and texture operations out alone,. And the major job ofdrawing is executed on GPU. Thus, compared with similar functions to other moleculesvisualization platform, the running speed of our platform has obviously improved.