Drug design dynamic simulation models

Standard molecular mechanics (MM) force fields have been developed that provide a good description of protein structure and dynamics,21 but they cannot be used to model chemical reactions. Molecular dynamics simulations are very important in simulations of protein folding and unfolding,22 an area in which they complement experiments and aid in interpretation of experimental data.23 Molecular dynamics simulations are also important in drug design applications,24 and particularly in studies of protein conformational changes,25,26 simulations of the structure and function of ion channels and other membrane proteins,27-29 and in studies of biological macromolecular assemblies such as F-l-ATPase.30... 

In these cases, i.e. when a direct comparison with experimental observables is not possible, the results of Molecular Dynamics simulations can be used to provide the numerical representation of structure (codified by stmctural descriptors) to be related with the experimental properties of interest through mathematical models. This implies a shift from empirical composition-property relationships to computational structure-property relationships, thus acquiring an immense practical importance in the development of predictive and interpretative models [16]. This approach, called Quantitative Structure-Property Relationships (QSPR), is well known and extensively applied in the area of drug discovery, and chemical toxicology modeling. However, its application in the field of material design is only recently being explored [17-19]. 

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