Chapter 23.1 Protein folds and motifs: representation, comparison and classification

Crystallography of biological macromolecules

First Online Edition (2006)

Part 23. Structural analysis and classification

  1. C. Orengo1,
  2. J. Thornton4,
  3. L. Holm2,
  4. C. Sander3

Published Online: 1 JAN 2006

DOI: 10.1107/97809553602060000714

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Orengo, C., Thornton, J., Holm, L. and Sander, C. 2006. Protein folds and motifs: representation, comparison and classification. International Tables for Crystallography. F:23:23.1:575–578.

Author Information

  1. 1

    Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, England

  2. 2

    Biochemistry and Molecular Biology Department, University College London, Gower Street, London WC1E 6BT, England, and Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, England

  3. 3

    EMBL–EBI, Cambridge CB10 1SD, England

  4. 4

    MIT Center for Genome Research, One Kendall Square, Cambridge, MA 02139, USA

Publication History

  1. Published Online: 1 JAN 2006


The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function. Domains are quasi-independent substructures that are thought to fold autonomously, to carry specific molecular functions, to move relative to each other as semi-rigid bodies and to speed the evolution of new functions by recombination. In the first part of this chapter, the classification of protein folds is discussed. In the second part of the chapter, the concepts underlying computational methods for locating domains in 3D structures are presented. Early algorithms focused on physical criteria to identify compact subunits. With the growth of the structural database, the focus has shifted to methods for identifying recurrent substructures that can form the basis for a consistent protein-structure classification.


  • protein domains;
  • protein structure classification