[37] Substrate docking algorithms and the prediction of substrate specificity
[37] Substrate docking algorithms and the prediction of substrate specificity
Publisher Summary This chapter describes the substrate docking algorithms and the prediction of substrate specificity. The utility of computer-assisted molecular docking for the prediction of cytochrome P450 substrates has been explored. P450cam is used as the model P450 enzyme because several high resolution crystal structures are available for it, although the approach should be applicable to any other isoform of P450 for which an active site structure is available. The chapter reviews computational approaches to analysis of the two subsequent steps, the degree of uncoupling, and the site specificity of the oxidation process. There are a number of programs available that can be used to predict whether a given small molecule will bind to a macromolecular receptor. DOCK has been used for the prediction of small molecules that bind to and inhibit a variety of enzymes. Future developments in this area should include utilization of the continuing improvements in ligand docking programs, such as, conformationally flexible searching, minimization of ligand/receptor complexes during searches, and more sophisticated scoring algorithms.
- University of California System United States
- University of California, San Francisco United States
- University of Queensland Australia
- University of Queensland Australia
Models, Molecular, 1303 Biochemistry, Binding Sites, Camphor 5-Monooxygenase, Databases, Factual, Molecular Structure, Protein Conformation, Ligands, Substrate Specificity, Kinetics, Models, Chemical, Drug Design, 1312 Molecular Biology, Algorithms
Models, Molecular, 1303 Biochemistry, Binding Sites, Camphor 5-Monooxygenase, Databases, Factual, Molecular Structure, Protein Conformation, Ligands, Substrate Specificity, Kinetics, Models, Chemical, Drug Design, 1312 Molecular Biology, Algorithms
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