A program that detects proteins with internal symmetry. SymD proved to be useful for analyzing protein structure, function and modeling. This web-based interactive tool was developed by implementing the SymD algorithm. It uses the Galaxy platform to take advantage of its extensibility and displays the symmetry properties, the symmetry axis and the sequence alignment of the structures before and after the symmetry transformation via an interactive graphical visualization environment in any modern web browser.
Discovers and sorts tandem repeat (TR) proteins and finds repeated structural modules from PDB files. RepeatsDB-lite is based on the ReUPred algorithm and can reduce errors in the unit detection step and speeding up the calculation. It is able to completely display the data including structural and sequence alignments of the predicted units. This tool allows users to refine the annotation and visualize the effect on the unit alignments on the fly.
Allows users to identify and analyze the internal symmetry and structural repeats in proteins. CE-symm is able to detect symmetry in proteins and define the boundaries of the structural repeating elements. It includes several features for: (1) comparing the similarity of all the internal repeats at the residue level; (2) describing the arrangement of repeats with transformation operations; (3) identifying the smallest repeating unit; and (4) reporting the type of symmetry.
A method for the detection of solenoid repeats from their amino-acid sequence. REPETITA is based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions. Parameters and thresholds were derived to allow the reliable discrimination of solenoid repeats from globular structures and the identification of their periodicities.
Finds internal repeats at three levels. Swelfe identifies repeats by alignment of DNA sequences, amino acids sequences and three dimensional (3D) structures. Preliminarily, 3D structures are encoded as linear sequences of α angles (α angle is the dihedral angle between four consecutive Cα). The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results.
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