This webserver is designed to do protein structure superimposition by various options. You can choose the following options to do superimposition:
  1. Ordered Residues
    -based on dihedral angle order paramter calculated by PDBStatTwoBoscPears.jpg
  2. Core Residues
    -based on interatomic variance matrix(IVM) calculated by FindCore
  3. Secondary Structure Element
    -Derived from PDB file keywords or DSSP calculation
  4. Arbitrary Selected Residue
    -User defined residues, formatted as 1A-11A,15A-40A
A superimposed structure ensemble would be generated for downloading.

Reference:

  1. 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.
  2. 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
  3. 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.
  4. 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.



The PDBStat/FindCore server is no longer supported.

A standalone version of PDBStat with FindCore2 is available for download and local installation on your computer at http://biopent.uv.es/~roberto/Index.php?sec=pdbstat