Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8. doi: 10.1093/nar/gkl092.


Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Internet
  • Protein Conformation*
  • Sequence Alignment / methods*
  • Software*
  • User-Computer Interface