Lysozyme Monte Carlo simulation

It is worthwhile to present some examples of the types of results available from Monte Carlo simulations of peptide solvent systems. In Figure 6 we present the convergence of the energy of hydration of the lysozyme crystal over a million configurations. 

Figure 6. The average energy of the water of hydration of the triclinic lysozyme crystal as a function of the number of configurations generated in the Monte Carlo simulation. The upper curve (A) corresponds to the cumulative statistical average, and the lower curve fU gives the statistical average over sequential sets of 5,000...

The algorithm was initially applied to docking PTl on the active side of trypsin, yielding a native-like mode of association among the top 12 solutions (Wodak and Janin, 1978). In five of six antibody-lysozyme and protease-inhibitor complexes, nativelike complexes were retrieved among the 10 highest scoring solutions by Monte Carlo simulated... 

The nucleation of thaumalin, trypsin, lobster a-crustatyanin, lysozyme, c-phycocyanin, myosin-binding protein-C, and a-actinin actin binding is aihanced in the presence of a porous medium nonporous surfaces are less successful at promoting nucleation (Chayen et al. 2006). Monte Carlo simulations confirmed that nucleation out of a filled pore is always faster than on a perfectly smooth surface, and the log of the rate varies almost linearly with pore size (Page and Sear 2006). 

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