Journal Article

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

David La, Juan Esquivel-Rodríguez, Vishwesh Venkatraman, Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt and Daisuke Kihara

in Bioinformatics

Volume 25, issue 21, pages 2843-2844
Published in print November 2009 | ISSN: 1367-4803
Published online September 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp542
3D-SURFER: software for high-throughput protein surface comparison and analysis

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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.

Journal Article.  1209 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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