Lecture GK-11

Structural alignment

Aims

• To describe methods for protein structural alignment.

Objectives

After this lecture you will:

• understand the purpose and methods of the SSAP and DALI structural alignment programs;
• know how to compute line segments that approximate the axes of helices and strands.

Supplementary Material

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

The SSAP program is described in: Taylor W.R. and Orengo C.A. (1989) "Protein structure alignment", J. Mol. Biol., 208, 1-22 (PubMed). The method used in SSAP is summarised in the lecture handout (local access only).

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 server web site.

A method for computing line segments that approximate the axes of helices and strands is described in: Singh A.P. and Brutlag, D.L. (1997) "Hierarchical protein structure superposition using both secondary structure and atomic representations", Proc. Int Conf. Intell. Syst. Mol. Biol., 5, 284-293 (Doug Brutlag's publication list).