Pairwise comparison of protein structures
This server computes optimal and suboptimal structural alignments between two protein structures using the DaliLite -pairwise option (version 3.1). It will compare all chains in the first structure against all chains in the second (unless chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol (requires Java).
You can use the Dali Server to search the whole PDB for structures which are similar to one query structure.
Precomputed structural alignments and database search results for all PDB structures are available from the Dali Database.
Upload first structure (mol1):
Or enter PDB identifier:   chain: (optional)
Upload second structure (mol2):
Or enter PDB identifier:   chain: (optional)
Most jobs finish within a minute.
Example
The comparison of beta-amylase (1byb) against itself reveals internal repeats. Tutorial
Notes
  • This server takes as input the atomic coordinates of a protein structure. Your file need only contain ATOM/HETATM entries, although full PDB format files are fine.
  • The structure must contain at least all backbone atoms (N, CA, C, O). If you have only the CA trace, use the MaxSprout server to generate full coordinates. The minimum chain length is 30 residues.
  • This server runs DaliLite v.3 in -p mode. Academic users may download the DaliLite program for local use.
  • The first and second structures are renamed mol1 and mol2 in results.
  • The URL of the results page is difficult to guess without knowledge of the input.
Reference
Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol. 19, 341-348.