Open AccessSuperPose: a simple server for sophisticated structural superposition
Author(s) -
R. Maiti,
Gary H. Van Domselaar,
Hong Zhang,
David S. Wishart
Publication year - 2004
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkh477
Subject(s) - biology , superposition principle , simple (philosophy) , web server , pairwise comparison , protein data bank (rcsb pdb) , sequence (biology) , range (aeronautics) , quaternion , interface (matter) , computer science , artificial intelligence , mathematics , engineering , world wide web , genetics , the internet , geometry , mathematical analysis , pulmonary surfactant , philosophy , biochemistry , gibbs isotherm , epistemology , aerospace engineering
The SuperPose web server rapidly and robustly calculates both pairwise and multiple protein structure superpositions using a modified quaternion eigenvalue approach. SuperPose generates sequence alignments, structure alignments, PDB (Protein Data Bank) coordinates and RMSD statistics, as well as difference distance plots and images (both static and interactive) of the superimposed molecules. SuperPose employs a simple interface that requires only PDB files or accession numbers as input. All other superposition decisions are made by the program. SuperPose is uniquely able to superimpose structures that differ substantially in sequence, size or shape. It is also capable of handling a much larger range of superposition queries and situations than many standalone programs and yields results that are intuitively more in agreement with known biological or structural data. The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/.
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