This webserver is designed to do protein structure superimposition by various options. You can choose the following options to do superimposition:
- Ordered Residues
-based on dihedral angle order paramter calculated by PDBStat
- Core Residues
-based on interatomic variance matrix(IVM) calculated by FindCore
- Secondary Structure Element
-Derived from PDB file keywords or DSSP calculation
- Arbitrary Selected Residue
-User defined residues, formatted as 1A-11A,15A-40A
A superimposed structure ensemble would be generated for downloading.
- Dihedral angle order parameters:Hyberts SG, Goldberg MS, Havel TF, Wagner G. The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci 1992; 1: 736-751.
- FindCore distance variance matrix:Snyder, D.A.; Montelione, G.T. "Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensemble". PROTEINS: Struct. Funct. Bioinformatics 2005, 59: 673-86
- Superimposition using Single Value Decomposition:Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr Sec A 1976; 32: 922-923.
- Second structure prediction:Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers 22(12): 2577-637
The underlying code used in this site was developed by R. Tejero, D. Synder, and G. Montelione as "PDBStat Sofware" and is available as standalone software from the authors.