3D-SURFER: software for high-throughput protein surface comparison and analysis

Bioinformatics. 2009 Nov 1;25(21):2843-4. doi: 10.1093/bioinformatics/btp542. Epub 2009 Sep 16.


Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized.

Availability: 3D-SURFER is a web application that can be freely accessed from: http://dragon.bio.purdue.edu/3d-surfer

Contact: dkihara@purdue.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Computational Biology / methods*
  • Databases, Protein
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism
  • Software*
  • Surface Properties


  • Proteins