By Valerie Daggett (Eds.)
Protein Simulation makes a speciality of predicting how protein will act in vivo. those experiences use laptop research, desktop modeling, and statistical chance to foretell protein functionality. * strength Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
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The diffuse nature of the true charge distribution and the fact that polarizability is more realistically spread over corresponding regions of space suggest that polarization should be damped at short range. The lack of damping in the Applequist model leads to failure of energetic models derived from it. The inability of the original Applequist scheme to adequately model the molecular polarizability of very polar, anisotropic molecules such as benzene is another symptom of the same problem (Applequist, 1993).
In section II, we review some of the history and performance of widely used protein force fields based on equation 1, or closely related equations. Sections III and IV outline some promising developments that go beyond this, primarily by altering the way electrostatics interactions are treated. Fig. 1. Schematic view of force field interactions. Covalent bonds are indicated by heavy solid lines, nonbonded interactions by a light, dashed line. 30 PONDER AND CASE Section III considers the use of atomic multipoles and off-center charge distributions, as well as attempts to incorporate electronic polarizability.
The iterative solution can generally be accelerated by well-known successive overrelaxation (SOR) techniques (Young, 1971) by using a value of ! 75 in equation 5, which converges rapidly to any reasonable level of accuracy. Þj; ðnÞ þ ! j; ðnÞ þ i j 0 ; ðnÞ f j0g A second method for finding the induced dipoles is full-matrix direct solution of the set of coupled linear equations, avoiding the iterative procedure. Also, in the context of molecular dynamics, the dipoles can again be updated via an extended Lagrangian scheme.
Protein Simulations by Valerie Daggett (Eds.)