Protein knot server: detection of knots in protein structures
By Grigory Kolesov, Peter Virnau, Mehran Kardar, Leonid A. Mirny. 2007
97 citations recorded by the source corpus.
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.
Subfields: Genetics, Geometry and Topology, Molecular Biology
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In Genetics
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In Molecular Biology
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Citations in the corpus
- Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “Candidate structures are also filtered to remove knotted structures as defined by computation of an Alexander polynomial by the KNOT server [59].”
- Energy functions in de novo protein design: current challenges and future prospects. (2013, background): “Most of these 78 knots are the simple three-point crossing (trefoil) knot, and the most complex is a six-point crossing knot for one protein called α -haloacid dehalogenase (the Stevedore knot) (55, 61).”
- 3D Protein Structure Predicted from Sequence (2011, unknown): “As we remove obviously knotted proteins [57]we would miss genuinely knotted proteins [58] which are however, rarely observed.”
- Using multiple templates to improve quality of homology models in automated homology modeling (2008, methodology): “To verify that this way of averaging coordinates does not introduce knotted or otherwise unphysical conformations, the output from Pfrag was screened for knots using the http://knots.mit.edu server (Kolesov et al. 2007).”