Molecular docking, computer-based

G. Wu, D. H. Robertson, C. L. Brooks, Detailed analysis of grid-based molecular docking A case study of CDOCKER-A CHARMm-based MD docking algorithm, J. Comput. Chem. 2003, 24, 1549-1562. 

III. Structure-based computational models of ligand-protein binding dynamics and molecular docking... 

In principle, molecular docking problems can be solved with molecular dynamics (MD) simulations. In fact, the earliest approaches for predicting protein-ligand interactions with the computer were based on MD calculations [100, 101]. 

Molecular docking and structural alignment methods are based on three-dimensional structures of candidate molecules that can be generated by rule-based methods such as CORINA [13, 14] or CONCORD [15]. However, methods based on three-dimensional structures are computationally quite demanding and cannot routinely be applied to databases of hundreds of thousands of compounds today. For this reason, a number of fast methods to determine molecular similarity have been developed that operate solely on connectivity and atom types of molecules. Such tools allow rapid prescreening of very large databases and avoid a conformational analysis of each candidate molecule. 

This chapter describes computational strategies for investigating the species in the catalytic cycle of the enzyme cjdochrome P450, and the mechanisms of its main processes alkane hydroxylation, alkene epoxidation, arene hydroxylation, and sulfoxidation. The methods reviewed are molecular mechanical (MM)-based approaches (used e.g., to study substrate docking), quantum mechanical (QM) and QM/MM calculations (used to study electronic structure and mechanism). 

Wu, G.S., Robertson, D.H., Brooks, C.L, and Vieth, M. (2003) Detailed analysis of grid-based molecular docking a case study of CDOCKER - a CHARMm-based MD docking algorithm. Journal of Computational Chemistry, 24, 1549—1562. 

Taufer M et al (2005) Study of an accurate and fast protein-ligand docking algorithm based on molecular dynamics. Concurr Comput 17(14) 1627-1641... 

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