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SymD
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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.
RAPHAEL
A method for the accurate determination of solenoid repeats from PDB structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified.
ReUPred / Repeat Protein Unit Predictor
A software tool for the classification and identification of repetitive elements in tandem repeat (TR) proteins. ReUPred concentrates on the solenoid proteins, since it is one of the most abundant class of tandem repeat proteins in nature. ReUPred extends the detailed annotation for all classified proteins in RepeatsDB and possibly for all predicted repeats. On a test set of solenoid proteins, it is able to correctly detect 92 % of the proteins. Unlike previous methods, ReUPred is also able to correctly classify solenoid repeats in 89 % of cases. It also outperforms two recent state-of-the-art methods for the repeat unit identification problem.
ConSole
A method to determine the presence and specific positions of individual solenoid repeat units within protein structures. Template matching, a popular image-processing procedure, applied to contact maps determines whether individual residues are part of a solenoid domain or part of a non-solenoid segment. This approach is further generalized to classify whether a whole protein structure under scrutiny is solenoid or non-solenoid. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool.
ProSTRIP
Finds similar structural repeats in a three-dimensional protein structure. ProSTRIP uses the protein backbone dihedral angles (computed using the four consecutive Cα atoms) for repeat detection. Further, the computed angles are translated into alpha characters for quick scanning. ProSTRIP uses a dynamic programming method to identify the internal sequence repeats. In addition to the detection of ungapped repeat stretch, the method has been designed with an additional feature of finding high scoring segment pairs (HSPs). An internet computing server is also created by implementing this method and enables graphical visualization of the results.
OPAAS
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A protein structure comparison (PSC) server with the functionality to report statistically significant alternative alignments and structural permutations at all levels of complexity. OPAAS deduces the probabilities of aligning every possible pair of secondary structure elements (SSEs) between two protein structures prior to the search for a solution of their alignment. This deduction allows the ready identification of most, though not all, statistically significant alignment solutions, many of which being distinct alternatives to the ‘optimal’ solution, the target of conventional PSC operations. Both permuted and non-permuted alternative alignments are reported by the OPAAS server in a fashion that is easy for a non-specialist user to grasp the main significance of the comparison as one would with the ‘optimal’ alignment featured by other PSC servers.
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