Approaches to the Docking Problem

In this section, we present an overview of the methods currently in use for docking binary protein complexes. Although docking of ternary protein complexes has been reported,36 the majority of computational studies to date deal with the case of two interacting proteins. 

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The GA approach has also been applied to the docking problem with dihydrofolatereduc-tase, arabinose binding protein, and sialidase... 

A.3 Search for the Correct Binding Mode (267-283). Just as there are many different approaches to the global minimization problem, most, if not all, have been applied to the docking problem. These include molecular dynamics, Monte Carlo sampling, systematic... 

Hybrid Methods Due to the complexity of the docking problem, all methods have their pros and cons. No one method will work well for every problem. Combining different methods is therefore a reasonable approach, which can result in methods containing the best of each. 

Carlo Simulation Approach to the Molecular Docking Problem. 

This section is dedicated to the scoring aspect of the docking problem. Various approaches are discussed that try to capture the essential elements of protein-ligand interactions in computationally efficient scoring functions. The discussion focuses on general approaches rather than individual functions. The reader is referred to Table 7.2 for original references to the most important scoring functions. 

Liu M, Wang SM. MCDOCK a Monte Carlo simulation approach to the molecular docking problem. J Comput-Aid Mol Des 1999 13 435-451. 

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