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Protein knot server
A web server that detects knots in protein structures. 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.
A server and database of proteins with lassos. LassoProt collects information about proteins and other (bio)polymers with lassos. LassoProt detects loops (closed by cysteine, as well as amide, ester, thioester and other bridges) in a given (bio)polymer, determines surfaces of minimal area spanned on such loops, and analyzes if and how termini of the polymer intersect these minimal surfaces. The server enables users to analyze new structures and includes a database, which presents extensive information about previously analyzed proteins with lassos.
Analyzes properties of lassos. PyLasso is a a PyMOL plugin that detects lassos in any biological, physical and mathematical systems, and provides various geometric characteristics thereof. The software enables analysis of trajectories. An additional feature is the function computing the Gaussian Linking Number, which measures how many times a part of the backbone chain winds around the closed loop. The software can be useful for researchers working on modeling of macromolecules, structure prediction, or properties of polymers for instance.
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