UNIT 5.5 Using Dali for Structural Comparison of Proteins

  1. Liisa Holm1,
  2. Sakari Kääriäinen1,
  3. Chris Wilton1,
  4. Dariusz Plewczynski2

Published Online: 1 JUL 2006

DOI: 10.1002/0471250953.bi0505s14

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Holm, L., Kääriäinen, S., Wilton, C. and Plewczynski, D. 2006. Using Dali for Structural Comparison of Proteins. Current Protocols in Bioinformatics. 14:5.5:5.5.1–5.5.24.

Author Information

  1. 1

    Institute of Biotechnology, University of Helsinki, Helsinki, Finland

  2. 2

    Interdisciplinary Centre for Mathematical and Computation Modeling, University of Warsaw, Warsaw, Poland

Publication History

  1. Published Online: 1 JUL 2006
  2. Published Print: JUN 2006


The Dali program is widely used for carrying out automatic comparisons of protein structures determined by X-ray crystallography or NMR. The most familiar version is the Dali server, which performs a database search comparing a query structure supplied by the user against the database of known structures (PDB) and returns the list of structural neighbors by e-mail. The more recently introduced DaliLite server compares two structures against each other and visualizes the result interactively. The Dali database is a structural classification based on precomputed all-against-all structural similarities within the PDB. The resulting hierarchical classification can be browsed on the Web and is linked to protein sequence classification resources. All Dali resources use an identical algorithm for structure comparison. Users may run Dali using the Web, or the program may be downloaded to be run locally on Linux computers.


  • classification of protein folds;
  • database searching;
  • distance geometry;
  • pattern recognition;
  • protein structure alignment