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

@article{citeulike:5998304, 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@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp542}, author = {La, David and Esquivel-Rodriguez, Juan and Venkatraman, Vishwesh and Li, Bin and Sael, Lee and Ueng, Stephen and Ahrendt, Steven and Kihara, Daisuke}, citeulike-article-id = {5998304}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp542}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/21/2843.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/21/2843.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19759195}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19759195}, day = {1}, doi = {10.1093/bioinformatics/btp542}, journal = {Bioinformatics}, keywords = {structure, structure-analysis}, month = {November}, number = {21}, pages = {2843--2844}, posted-at = {2009-10-25 07:45:29}, priority = {2}, title = {3D-SURFER: software for high-throughput protein surface comparison and analysis}, url = {http://dx.doi.org/10.1093/bioinformatics/btp542}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:5998304 L3 - citeulike-article-id:5998304 N2 - 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. 10.1093/bioinformatics/btp542 IS - 21 JF - Bioinformatics EP - 2844 TI - 3D-SURFER: software for high-throughput protein surface comparison and analysis VL - 25 SP - 2843 KW - structure KW - structure-analysis AU - La, David AU - Esquivel-Rodriguez, Juan AU - Venkatraman, Vishwesh AU - Li, Bin AU - Sael, Lee AU - Ueng, Stephen AU - Ahrendt, Steven AU - Kihara, Daisuke PY - 2009/11/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp542 ER -