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.
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.
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.
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.
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.
Provides an elegant and computationally efficient graph-based approach for detecting Ankyrin structural repeats in proteins. By analyzing the eigen spectra of the protein structure graph and secondary structure information, characteristic features of a known repeat family are identified. AnkPred is especially useful in correctly identifying new members of a repeat family.
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.