| advertisement: compare things at compare-stuff.com! |
The technique known as docking applies knowledge of protein surfaces and interactions to predict the location, orientation and conformation of ligands in their physiological interactions with proteins. This is a huge field with many methods currently in development. The principles and methods of docking are reviewed in Bamborough and Cohenbamborough:dockreview. The extent of its success is variable and has not been rigorously tested (see Section 1.4.5, however). One major problem is predicting the conformational changes in protein and ligand which are often observed on binding through crystallographic studies, a problem not far removed from ab initio structure prediction described in the following section. Furthermore, the evaluation of ligand-protein energetics is not yet fast enough or accurate enough to reliably identify the correct binding mode from the massive number of alternative orientations which must be generated if the binding site is not known.