Pre-calculated protein structure alignments at the RCSB PDB website

Bioinformatics. 2010 Dec 1;26(23):2983-5. doi: 10.1093/bioinformatics/btq572. Epub 2010 Oct 10.


Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.

Availability and implementation: A web user interface is available at The source code is available under the LGPL license from A source bundle, prepared for local execution, is available from


Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Databases, Protein*
  • Internet
  • Proteins / chemistry
  • Software*
  • Structural Homology, Protein*
  • User-Computer Interface


  • Proteins