The Docking Problem

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. 

Throughout this chapter, we roughly separate docking approaches by their treatment of protein flexibility. Within the two broad categories (rigid body and flexible docking), the docking problem can be separated into two subproblems ... 

Refinement of Protein Interfaces Incorporating Solvation Application to the Docking Problem. 

Jackson RM, Sternberg MJ. A continuum model for protein-protein interactions application to the docking problem. J. Mol. Biol. 81. 1995 250 258-275. 

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... 

To address the docking problem, techniques for a more global exploration of the en-ag/ landscape are required. A variety of methods is available, frequently used in the context cf other modeling applications and optimization problems as well. Three major classes may be distinguished Monte Carlo techniques, molecular dynamics simulations, and genetic algorithms. Many different vari-fants exist for all of them and frequently, in... 

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. 

Sotriffer, C., Stahl, M. and Klebe, G. (2003) The docking problem, in Handbook of Chemoirfonnatics, Vol. 4 (ed. J. Gasteiger), Wdey-VCH Verlag GmbH, Weinheim, Germany pp. 1732-1768. 

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