Lecture 10

Docking; Channels; Multi-resolution modelling

Aims

• To describe a polyhedral representation of macromolecular shape and its application in predicting binding surfaces.
• To describe a method for combinatorial docking.
• To introduce structural proteomics.
• To introduce the problem of finding channels in proteins.

Objectives

After this lecture you will be able to:

• describe how a probe sphere is used in defining a polyhedral representation of a protein's shape;
• discuss how propensities can be used to predict binding sites;
• explain how combinatorial docking can be used to predict the conformations of large macromolecular complexes;
• describe the problem of fitting high-resolution molecular structures into envelopes derived from low-resolution data.
• describe the problem of finding channels in proteins.

Supplementary Material

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

A brief description of the molecular polyhedral shape representation program is given in an appendix of my PhD thesis (PDF, local access only).

Surface triplet propensities are described in: Mehio, W., Kemp, G.J.L., Taylor P. and Walkinshaw, M.D. (2010) Identification of protein binding surfaces using surface triplet propensities. Bioinformatics, 26, 2549-2555 ( doi:10.1093/bioinformatics/btq490)

An approach to combinatorial docking is described in: Inbar, Y., Benyamini H., Nussinov R. and Wolfson H.J. (2005) Prediction of multimolecular assemblies by multiple docking. J. Mol. Biol., 349, 435-447 (doi:10.1016/j.jmb.2005.03 .039)

"The Inner Life of a Cell" is the result of a collaboration between scientists at Harvard University and a scientific animation company. An extended version with commentary is available on the Harvard University web site.