Aims

• To introduce the terms used in calculating a molecule's potential energy.
• To introduce Monte Carlo methods and simulated annealing.
• To introduce the ab initio protein folding problem.
• To give an overview of the protein structure prediction method of Simons et al. (1997).

Objectives

After this lecture you will:

• know the terms that are typically used in a potential energy function;
• understand the Metropolis procedure and simulated annealing;
• be aware of the the ab initio protein folding problem;
• understand in outline the protein structure prediction algorithm of Simons et al. (1997).

Supplementary Material

Michael Levitt has produced some useful lecture slides that include descriptions of the protein folding problem, molecular simulation and structure prediction by energy minimisation.

There is an on-line description of simulated annealing and the Metropolis algorithm at:

Eric W. Weisstein et al. "Simulated Annealing." From MathWorld--A Wolfram Web Resource. http://mathworld.wolfram.com/SimulatedAnnealing.html

The ab initio protein structure prediction algorithm introduced in this lecture is described in:

Simons, K.T., Kooperberg, C., Huang, E. and Baker, D. (1997) Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences using Simulated Annealing and Bayesian Scoring Functions. J. Mol. Biol., 268, 209-225 (PubMed)