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Bioinformatics Advance Access originally published online on September 16, 2009
Bioinformatics 2009 25(21):2843-2844; doi:10.1093/bioinformatics/btp542
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

David La 1,{dagger}, Juan Esquivel-Rodríguez 2,{dagger}, Vishwesh Venkatraman 1, Bin Li 2, Lee Sael 2, Stephen Ueng 2, Steven Ahrendt 1 and Daisuke Kihara 1,2,3,*

1 Department of Biological Sciences, 2 Department of Computer Science and 3 Markey Center for Structural Biology, College of Science, Purdue University, West Lafayette, IN 47907, USA

* To whom correspondence should be addressed.


  Abstract

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{at}purdue.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First authors.

Associate Editor: Anna Tramontano

Received on June 12, 2009; revised on July 24, 2009; accepted on September 10, 2009

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