Ligand-receptor docking with the Mining Minima optimizer.
The optimizer developed for the Mining Minima algorithm, which uses ideas from Genetic Algorithms, the Global Underestimator Method, and Poling, has been adapted for use in ligand-receptor docking. The present study describes the resulting methodology and evaluates its accuracy and speed for 27 test systems. The performance of the new docking algorithm appears to be competitive with that of previously published methods. The energy model, an empirical force field with a distance-dependent dielectric treatment of solvation, is adequate for a number of test cases, although incorrect low-energy conformations begin to compete with the correct conformation for larger sampling volumes and for highly solvent-exposed binding sites that impose little steric constraint on the ligand.
Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA.
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L
David
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Luo
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MK
Gilson
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D011956:Receptors, Cell Surface / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity; D013816:Thermodynamics
D008024:Ligands; D011956:Receptors, Cell Surface