6533b7ddfe1ef96bd1274ac2

RESEARCH PRODUCT

Protein knot server: detection of knots in protein structures

Peter VirnauGrigory KolesovMehran KardarLeonid A. Mirny

subject

Models MolecularWeb serverProtein FoldingTheoretical computer scienceProtein ConformationProtein Data Bank (RCSB PDB)MathematicsofComputing_NUMERICALANALYSISAlexander polynomialBiologyBioinformaticscomputer.software_genreUploadUser-Computer InterfaceKnot (unit)Protein structureTheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITYComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATIONGeneticsComputer SimulationSurgical knotsDatabases ProteinInteractive visualizationComputingMethodologies_COMPUTERGRAPHICSInternetQuantitative Biology::BiomoleculesModels StatisticalComputational BiologyProteinsArticlesHaemophilus influenzaeMathematics::Geometric TopologycomputerAlgorithmsSoftwareMathematicsofComputing_DISCRETEMATHEMATICS

description

KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regularly updated list of known knots in protein structures.

yearjournalcountryeditionlanguage
2007-05-01
10.1093/nar/gkm312http://hdl.handle.net/1721.1/72331