Piecewise linear energy function

Figure 3 The frequency of predicting the crystal structure of the SB203386-HIV-1 protease complex in docking simulations with the ensemble of 6 protein conformations (a) and the ensemble of 32 protein conformations (b). The RMSD of the docked inhibitor conformations from the crystal structure ranked by energy in simulations with the ensemble of 6 protein conformations (c) and the ensemble of 32 protein conformations (d). The piecewise linear energy function is employed.

Figure 6 The binding free energy landscape for SB203386 generated with the piecewise linear energy function and the ensembles of 6 protein conformations (a) and 32 protein conformations (b). For each two-dimensional temperature slice, the reference energy F R = 0,T) is defined to be zero.

In PLPscore, both the steric and hydrogen bonding terms are calculated from a piecewise linear potential function (see Fig. 1), instead of a smooth 6-12 Lennard-Jones potential energy function. The difference between the two terms is simply in the parameter values chosen for each term. 

The code SPECTRA assumes that the flux is a piecewise-linear function of energy i.e., for any energy group j, one can write... 

FIGURE 1.211 Distribution functions of the activation energy of the mobility of water molecules at a surface of polymer LiChrolut EN adsorbent calculated on the basis of the NMR data (curve 1, hydration h=2 g/g) and dipolar and dc relaxation (TSDC, curves 2 (regularization) and 3 (piecewise linearization), h=5A g/g). (Adapted from Colloids Surf. A.- Physicochem. Eng. Aspects, 336, Gun ko, V.M., Turov, V.V., Zarko, V.I., Goncharuk, E.V., and Turova, A.A., Regularities in the behaviour of water confined in adsorbents and bioobjects studied by NMR spectroscopy and TSDC methods at low temperatures, 147-158, 2009e. Copyright 2009, with permission from Elsevier.)... 

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