Indexing methods for efficient protein 3D surface search
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics
Fast protein 3D surface search
Proceedings of the 7th International Conference on Ubiquitous Information Management and Communication
Interactive extraction and tracking of biomolecular surface features
EuroVis '13 Proceedings of the 15th Eurographics Conference on Visualization
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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.