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• INTRODUCTION
  
  SCide is a server to identify stabilization centers in proteins. These are clusters of residues involved in long-range interactions. Because of the cooperative nature of these interactions, they are likely to play an important role in maintaining the stability of protein structures.

  The definition of stabilization centers is the following:
  

  • Two residues are in contact if there is at least at least one heavy atom-atom distance smaller than the sum of their van der Waals radii plus 1 A.
  
  
  • A contact is recognizied as "long-range" interaction if the interacting residues are at least 10 amino acids apart.
  
  
  • Two residues are form a stabilization center if they are in long-range interaction, and if it is possible to select one-one residues from both flanking tetrapeptides of these two residues that make at least seven contacts between these two triplets.
    
  
  

  References:
  Zs. Dosztányi, A. Fiser & I. Simon
  J. Mol. Biol. 272 (4) 597-612.
  
  Zs. Dosztányi, Cs. Magyar, G. E. Tusnády & I. Simon
  SCide: identification of stabilization centers in proteins.
  Bioinformatics (2003) 19:899-900.
  

  
  
• PDB STRUCTURE
  
  PDB files are specified by its four letter code
(e.g. 16pk)
You can search for PDB files at the Protein Data Bank


• UPLOAD A FILE
  
  You may upload a PDB file from your computer. Please note that this option only works with Netscape Browsers or Internet Explorer version 5 or later. Click here to download an example pdb file.



• SPECIFY A REGION
  
  The analysis of interactions can be narrowed to specific regions, or between two regions. The selection can be made for chains or by explicitly by giving the beginning and the end of the region by their residue numbers. In default the whole molecule given in the PDB file is used.



• RESIDUE NUMBERING
  
  Residue numbering in the PDB files can be quite peculiar, including cases of insertions, negative numbers, insertions within gap (!). This all could be meaningful in a specific context, but it is a nightmare if one wants to identify a residue. Here, each residue is numbered sequentially starting from one for each chain. Alternatively, the PDB numbering can also be used. Please note, this includes the insertion code, if it is given is the original PDB file for that residue.



• OUTPUT TYPE
  
  This option lets you choose two types of text output. The graphical option is temporarly not available. The default value is text output, this simply lists the amino acids in the specified region, and gives all the partner amino acids for stabilization centers. 



• RELATED LINKS
  
  PDB Protein Data Bank
  PQS Protein Quarternary Structure
  ProTherm: Thermodynamic Database for Proteins and Mutants