3D-SURFER is web-based software for protein surface comparison and analysis. The server integrates various repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. It takes less than a second to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB. Conveniently, the web interface also renders animated protein rotations, displays CATH codes [Orengo CA, Structure, 1997], and structure alignment calculations using the Combinatorial Extension (CE) algorithm [Shindyalov IN and Bourne PE, Protein Eng, 1998]. Please check out our tutorial slides on how to use 3D-SURFER!
3D-SURFER provides an interactive web-based platform for high throughput comparision and analysis of protein surfaces. 3D-Zernike Descriptors (3DZD) are utilized for the efficient comparison of protein surfaces [Sael L, Proteins, 2008] across the entire PDB. Results can be interactively analyzed using various features provided by the visibility criterion [Li B, Proteins, 2007]. Please refer to our documentation page for more information about the methods used in this server.
All latest web browsers (Mozilla, Firefox, Safari, Opera, Internet Explorer, etc) are supported. In addition, the server utilizes Jmol to visualize protein structures and surfaces. Please make sure you install Java on your computer and enable Java applet support for your browser.