How does one help researchers visualize the proteins with which they are working to facilitate understanding and hypothesis testing?
We help researchers by creating images of proteins which are colored to accentuate protrusions and cavities. Follow the link to programto get started right away and for more detailed information about its functions. galleryshows several images so that you can see if these visualizations are what you want. Below is more informationabout the Summer 2007 R2 project.
It is widely believed that a protein's functionality is to a large extent decided by its three-dimensional structure (the conformation it forms in three-space). Hence accurate modeling of protein 3D structure becomes an important task in current post-genomic era. Informatiive visualization can help to display, not only geometric, but also various bio-chemical properties of input molecules. This project aims at building a web tool for molecular visualization that is easy to use for a wide range of users. Many molecular visualization tools exist in the scientific community: such as RasMol, VMD, Chime, and so on. Most of them focus on displaying the chemical composition of input molecules, and provide relatively simply visualization of the three-dimensional molecular structure. Our software, instead, focuses on providing a platform where we can visualize various descriptors (modeling various properties) over input structures. For example, we display geometric shape descriptors that capture features such as cavities and protrusions of the input molecular surfaces, which emphasize possible docking sites for other molecules. The software will run within a website, and will not require downloading the program, ensuring researchers easy access to this resource.
Note: You need Java3d to run this program. Go to the Java Sun page to download Java3d.