3VND

Structural Similarities for the Entities in PDB 3VND

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].

Currently viewing only significant results (P-value < 0.001). Show all available results.

Cluster data are up-to-date as of: Sep-27-2017

• [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 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. (2008).
  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.