Internal symmetry detection software tools | Protein structure data analysis
Internal symmetry of a protein structure is the pseudo-symmetry that a single protein chain sometimes exhibits. This is in contrast to the symmetry with which monomers are arranged in many multimeric protein complexes.
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.
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.
Consists in an algorithm serving for non-sequential structural alignment of proteins and similarity search in databases. GANGSTA+ is able to notice structural similarities between two proteins, although their sequences might be reshuffled during evolution. It can spot non-sequential structural analogs for proteins stated to possess novel folds. Its online interface provides several functions: (1) comparing structures of a pair and performing a score; (2) searching the database; and (3) browsing the database.
Detects symmetry of proteins on clusters of computers. Parallel-SymD is a parallelized algorithm that identifies symmetry in protein domains and is especially suited to execution on multiple central processing units (CPUs) and computer of varying power interconnected in a network. Its only requirement is that the program has to be properly installed and that the master node has to be able to communicate with all slave nodes through the MPI library.
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.