Lecture 9

Lattice models; fold recognition; molecular surface; channels

Aims

• To introduce lattice models for exploring protein folding.
• To introduce fold recognition.
• To introduce the concepts of solvent accessible surface and molecular surface.
• To introduce the problem of finding channels in proteins.

Objectives

After this lecture you will be able to:

• discuss lattice models and their use in structural bioinformatics;
• describe in outline the threading method for fold recognition;
• explain the concepts solvent accessible surface and molecular surface;
• describe the problem of finding channels in proteins.

Supplementary Material

Some lecture slides on lattice models.

A detailed description of the derivation of pairwise potentials is given in: Sippl, M.J. (1990) Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins", 213, 859-883 (doi:10.1016/S0022-2836(05)80269-4)

The solvent accessible surface was proposed in: Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol., 55, 379-400 (doi:10.1016/0022-2836(71)90324-X). Calculation and visualisation of the solvent accessible surface and the molecular surface is discussed in an interesting review article by Michael Connolly.