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!

Latest features:

  • CATH code filtering: It is common that the results returned are very similar, in terms of the CATH codes they have. If the user wants, for example, to get results that are different in terms of the first two levels (specify CATH filter as "CA"), then the query will avoid returning repeated results for structures that share the first two levels. In other words, if two structures have CATH codes 3.40.390.10 and, only one of them would be returned, because 3.40 is repeated.
  • Length filtering: When "Residue Length Filter" is enabled, the results returned will be similar in terms of the number of residues that each structure has. Two structures are considered similar if the size of one with respect to the other is between 0.57 and 1.75 times the size of the other one.


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.