Conformation sampling Monte Carlo simulations

The hst which follows gives an outline of the properties of a Monte Carlo simulation used in the context of molecular modeling studies for sampling either multiple conformations of smaller, flexible stmctures or multiple local minima of larger macromolecules or polymers ... 

Fig. 7. Pocket fumigation is a modeling technique based on torsional sampling in the presence of a repulsive density representing a generic ligand, (a) the original X-ray structure (b) the result of Ala conversion the largest pocket density is generated (c) a druggable" pocket conformation obtained by Monte Carlo simulation in the presence of the density.

A novel approach to protein conformation is the entropy-sampling Monte Carlo method (ESMC), which is described in detail in another contribution to this volume. The method provides a complete thermodynamic description of protein models, but it is computationally quite expensive. However, because of the underlying data-parallel structure of ESMC algorithms, computations could be done on massively parallel computers essentially without the communication overhead typical for the majority of other simulation techniques. This technique will undoubtedly be applied to numerous systems in the near future. 

Random sampling, an approach in molecular modeling for conformational energy searching that relies on stochastic probing (Monte Carlo simulation). Different conformations are examined at random - in contrast to systematic searching - in order to explore the conformational space of a molecule. 

Details on how to perform the calculations are given in [18], Here, it shall be sufficient to roughly describe the procedure Conformational sampling is performed by an in-house Monte-Carlo/simulated annealing algorithm ]36], based on the MMFF94s ]37-38] forcefield as implemented in Sybyl ]39], Typically, the Fukui ffinctions of different conformers do not exhibit different features... 

Formaldehyde in 95 samples of lady pajamas collected in Chinese market was detected and distribution characteristics of formaldehyde content was analyzed using Oracle Crystal Ball 11.1 software and results showed that the formaldehyde concentration conforms to the Max Extreme distribution most. The risk assement model of formaldehyde in domestic textile was established using the Monte Carlo simulation technique. The model was applied to the practice and the result showed that cumulative probability of risk of being exposed to formaldehyde in pajamas through the skin less than 10 is 98.69%, so the risk can be ignored. 

The random nature of Monte Carlo simulation makes it a useful tool for sampling conformational space. Although the efficiency of sampling conforma-... 

---