Chapter 23.2 Locating domains in three-dimensional structures

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 23. Structural analysis and classification

  1. L. Holm1,
  2. C. Sander2

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000891

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Holm, L. and Sander, C. 2012. Locating domains in three-dimensional structures. International Tables for Crystallography. F:23:23.2:752–754.

Author Information

  1. 1

    EMBL–EBI, Cambridge CB10 1SD, England

  2. 2

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

Publication History

  1. Published Online: 14 APR 2012


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. The concepts underlying computational methods for locating domains in three-dimensional 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