Modeling enzyme reactions

Mulholland AJ (2005) Modelling enzyme reaction mechanisms, specificity and catalysis. Drug Discov Today 10 1393-1402... 

Quantum Chemical Approaches to Modelling Enzyme Reactions Cluster (or Supermolecule) Approaches... 

While it is possible to develop MM parameters specifically for reactions, but this is highly laborious, and the resulting parameters may not be transferable. Also, the form of the potential function can impose serious limitations, such as the neglect of electronic polarization. Methods that take the fundamental quantum mechanics of electronic structure into account are more generally applicable. Quantum mechanical methods (i.e. methods to calculate molecular electronic structure) are often preferable and can be easier to apply than involved molecular mechanics type approaches. The major problem with electronic structure calculations on enzymes is the large computational resources required, which significantly limits the size of the system that can be treated. Quantum chemical approaches to modelling enzyme reactions are described in the next couple of sections. 

Enzyme catalyzed reactions can also be modeled using the empirical valence bond (EVB) method [21]. EVB methods are central in modeling enzyme reactions and catalysis. They are reviewed well elsewhere [22,12] and so are not the focus of this review. 

Siegbahn P, Himo F (2011) The quantum chemical cluster approach for modeling enzyme reactions. WIREs Comput Mol Sci 1 323... 

The paper written by Warshel and Levitt [162] introduced the first QM/MM concept. Since about 1990, QM/MM approaches have been used by many groups, in particular for modelling enzyme reactions, but also for other catalytic reactions, for example, in zeolites [163]. QM/MM methods are established as a powerful computational technique to treat reactive processes in large systems. They are... 

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