Knot detection software tools | Protein structure data analysis
Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank (PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol-acid reductoisomerase or SpoU methyltransferase.
Provides a structural database of knotted proteins, analysis tools for detecting and analyzing knotted regions from structures as well as a Java-based 3D graphics viewer for visualizing knotted structures. A homology modeling tool has been implemented such that the server can accept protein sequences in addition to 3D structures or Protein Data Bank (PDB) IDs and return knot analysis.
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.
Aims to analyze and classify open spatial curves. Knoto-ID can be applied to study any open linear conformation in 3-space such as chromosomes, synthetic polymers, or random walks. This tool is able to manage closed chains as input, or to create a closed chain from an open one using either direct and uniform closure. Moreover, it can analyze all subchains of a given curve to produce a fingerprint matrix for the case of open chains or a disc matrix.
Allows users to identify the deterministic, probabilistic and macromolecular links in proteins. PyLink furnishes a method for finding links in automatic mode and in manual mode, giving users the freedom to specify linked components. This tool can search for closed loops formed by a few covalent bridges or interaction via ions.
A flexible R package providing tools for the detection and characterization of topological knots in proteins and others polymers. The package is well documented and provides a simple syntax for data import and preprocessing, structure reduction, topological analyses and 2D and 3D visualization. Rknots is not limited to protein knots and allows researchers from interdisciplinary fields to analyze different topological structures and to develop simple yet fully custom pipelines.