Structural Bioinformatics

Graham Kemp > Teaching > Structural Bioinformatics

Lecture GK-4

Structure comparison; efficient distance checks

Aims

To describe methods for protein structure comparison.
To introduce different methods for checking for steric overlap in molecular structures.

Objectives

After this lecture you will:

understand the purpose and methods of the SSAP and DALI structure comparison programs;
be aware of different methods for checking for steric overlap when modelling proteins.

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. 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.