Physical principles interatomic interactions

Although knowledge-based potentials are most popular, it is also possible to use other types of potential function Some of these are more firmly rooted in the fundamental physics of interatomic interactions whereas others do not necessarily have any physical interpretation at all but are able to discriminate the correct fold from decoy structiu-es. These decoy structures are generated so as to satisfy the basic principles of protein structure such as a close-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly important in threading. For practical purposes the library should obviously not be too large, but it should be as representative of the different protein folds as possible. To derive a fold database one would typically first use a relatively fast sequence comparison method in conjunction with cluster analysis to identify families of homologues, which are assiuned to have the same fold. A sequence identify threshold of about 30% is commonly... 

Pair-additive interactions continued to be used in most materials-related simulations for over 20 years after Vineyard s work despite well-known deficiencies in their ability to model surface and bulk properties of most materials. Quantitative simulation of materials properties was therefore very limited. A breakthrough in materials-related atomistic simulation occurred in the 1980s, however, with the development of several many-body analytic potential energy functions that allow accurate quantitative predictions of structures and dynamics of materials.These methods demonstrated that even relatively simple analytic interatomic potential functions can capture many of the details of chemical bonding, provided the functional form is carefully derived from sound physical principles. 

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