Lecture GK-4

Protein domains

Aims

• To introduce the concept of structural domains.
• To describe how domains can be assigned automatically.

Objectives

After this lecture you will:

• know that proteins often consist of structural domains;
• know how to interpret distance maps;
• understand, in outline, how domain assignment can be performed.

Supplementary Material

Some of the lecture slides are available on-line (PDF).

Several distance maps are shown on The Protein Kinase Resource web site.

The algorithm used by DOMAK to identify structural domains is described in:

Siddiqui, A.S. and Barton G.J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Science, 4, 872-884. (PubMed)

The algorithm used by STRUDL to identify structural domains is described in:

Wernisch, L., Hunting, M. and Wodak, S.J. (1999) Identification of structural domains in proteins by a graph heuristic. Proteins: Structure, Function and Genetics, 35, 338-352. (Pubmed)

Voronoi diagrams are described at MathWorld.