Lecture 8

Molecular mechanics; Monte Carlo algorithms

Aims

• To introduce the terms used in calculating a molecule's potential energy.
• To introduce Monte Carlo methods, the Metropolis criterion, and simulated annealing.
To introduce the structural alignment problem.

Objectives

After this lecture you will be able to:

• discuss some of the terms used in calculating a molecule's potential energy;
• describe Monte Carlo methods and simulated annealing.

Supplementary Material

Michael Levitt has produced some excellent lecture slides that include descriptions of the protein folding problem, molecular simulation and structure prediction by energy minimisation. Levitt has also written about the history of computational structural biology:

Levitt, M. (2001) The birth of computational structural biology. Nature Structural Biology, 8, 392-393 (doi:10.1038/87545)

including the first applications of protein energy minimisation:

Levitt, M. and Lifson, S. (1969) Refinement of protein conformations using a macromolecular energy minimization procedure. J. Mol. Biol., 46, 269-279 (doi:10.1016/0022-2836(69)90421-5)

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

Carr, Roger "Simulated Annealing." From MathWorld--A Wolfram Web Resource, created by Eric W. Weisstein. http://mathworld.wolfram.com/SimulatedAnnealing.html