Aims

• To describe a method for protein structure comparison.
• To describe methods for protein fold recognition.

Objectives

After this lecture you will:

• understand the purpose and method of the DALI structure comparison program;
• understand the purpose and methods of different protein fold recognition programs.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line. (PDF)

For more information about the DALI algorithm for pairwise protein structure alignment, see the article "Mapping the Protein Universe" by Liisa Holm and Chris Sander (Science vol. 273, 595-602, 1996), and the DALI web site.

Some protein fold recognition servers are listed on the links page of the Protein Structure Prediction Center web site. For more information on fold recognition and threading, I recommend the following early articles:

Bowie, J.U., Lüthy, R. and Eisenberg, D. (1991) A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure. Science, 253, 164-170.

Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.

Sippl, M.J. and Weitckus, S. (1992) Detection of Native-Like Models for Amino Acid Sequences of Unknown Three-Dimensional Structure in a Data Base of Known Protein Conformations. Proteins: Structure, Function and Genetics, 13, 258-271.