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


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


BACKGROUND
dkihara@purdue.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
La
David
D
Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN 47907, USA.
Esquivel-Rodríguez
Juan
J
Venkatraman
Vishwesh
V
Li
Bin
B
Sael
Lee
L
Ueng
Stephen
S
Ahrendt
Steven
S
Kihara
Daisuke
D
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013499:Surface Properties
D011506:Proteins