The following structural similarities have been found using the jFATCAT-rigid algorithm [1,2]. To reduce the number of hits, a 40% sequence identity clustering has been applied and a representative chain taken from each cluster. If the representative chain consists of multiple domains, each domain is included in the search. If available, the SCOP 1.75 domain assignment [3] is used. Otherwise algorithmic domain assignments are computed using the ProteinDomainParser [4].

• References

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  [1] Andreas Prlić; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
  Pre-calculated protein structure alignments at the RCSB PDB website  
  Bioinformatics 26: 2983-2985

  [2] The all vs. all comparisons are based on jFATCAT, a Java port of the original FATCAT algorithm   see:

  Yuzhen Ye & Adam Godzik (2003)
  Flexible structure alignment by chaining aligned fragment pairs allowing twists.  
  Bioinformatics vol.19 suppl. 2. ii246-ii255.

  [3] Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2007).
  Data growth and its impact on the SCOP database: new developments.  
  Nucl. Acids Res. 2008 36: D419-D425;

  [4] Alexandrov N., Shindyalov I. (2003)
  PDP: protein domain parser.  
  Bioinformatics 2003 Feb;19(3);429-30.

   

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• Update Status

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  Jan 13 2015

  
  Cluster data are up-to-date as of:

   

• Table Legend

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  • Rank: current row position. Changes with different sorting orders and filter rules
  • Domain 2: Domain name of 2nd domain. Can be either a SCOP ID (d<PDB ID><Chain ID><Domain ID>), ProteinDomainParser ID (PDP:<PDB ID><Chain ID><Domain ID>)
  • Title: Protein chain description
  • P-value: P-value of this alignment (FATCAT) (default sorted by this)
  • Score: Raw alignment score (FATCAT)
  • RMSD: RMSD value of the alignment
  • Len1: Domain 1 length
  • Len2: Domain 2 length
  • %ID: % sequence identity in the alignment. A 40% sequence identity filter is applied before the structure alignments are calculated, so most results show low similarity. If the sequences are of vastly different lengths, the clustering procedure will group them in different clusters, even if they share a region of high sequence similarity.
  • %Cov1: The coverage, or %, of aligned residues in chain 1
  • %Cov2: The coverage, or %, of aligned residues in chain 2

  The table is sorting is by P-value by default. Clicking on the column header will change the sort order. Select the Filter Results icon to apply other filtering criteria.

   

Documentation

A detailed description of the procedure for the all vs. all alignments is available.