Areas of Application
One of the molecular mechanics application is energy minimization. That is, the force field is used as an optimization criterion and the (local) minimum searched by an appropriate algorithm (e.g. steepest descent). Global energy optimization can be accomplished using simulated annealing, the Metropolis algorithm and other Monte Carlo methods, or using different deterministic methods of discrete or continuous optimization. The main aim of optimization methods is finding the lowest energy conformation of a molecule or identifying a set of low-energy conformers that are in equilibrium with each other. The force field represents only the enthalpic component of free energy, and only this component is included during energy minimization. However, the analysis of equilibrium between different states requires also conformational entropy be included, which is possible but rarely done.
Molecular mechanics potential energy functions have been used to calculate binding constants, protein folding kinetics, protonation equilibria, active site coordinates, and to design binding sites.
Read more about this topic: Molecular Mechanics
Famous quotes containing the words areas of, areas and/or application:
“The point is, that the function of the novel seems to be changing; it has become an outpost of journalism; we read novels for information about areas of life we don’t know—Nigeria, South Africa, the American army, a coal-mining village, coteries in Chelsea, etc. We read to find out what is going on. One novel in five hundred or a thousand has the quality a novel should have to make it a novel—the quality of philosophy.”
—Doris Lessing (b. 1919)
“Adults understandably assume that the level of verbal proficiency a five-year-old displays represents his level of proficiency in all areas of functioning—if he talks like an adult, he must think and feel like one. However, five-year-olds,... belie the promise of adult-like behavior with their child-like, impulsive actions.”
—Dorothy H. Cohen (20th century)
“Courage is resistance to fear, mastery of fear—not absence of fear. Except a creature be part coward it is not a compliment to say it is brave; it is merely a loose application of the word. Consider the flea!—incomparably the bravest of all the creatures of God, if ignorance of fear were courage.”
—Mark Twain [Samuel Langhorne Clemens] (1835–1910)