Comparison of database potentials and molecular mechanics force fields.
The advantages and disadvantages of database and molecular mechanics force fields for the study of macromolecules are compared, with emphasis on the ability to distinguish between correct and incorrect structures. Molecular mechanics force fields have the advantage of resting on a clear theoretical basis, permitting an in-depth analysis of different contributions. On the other hand, large simplifications are necessary for tractable computing, and there has so far been little effective testing at the macromolecular level. Database potentials allow greater freedom of functional form and have been shown to be effective at discriminating between correct and incorrect complete structures. The principal negative is a controversial relationship to free energy. More testing and comparison of both sorts of potential are needed.
Moult
J
J
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA. jmoult@indigo5.carb.nist.gov
D016208:Databases, Factual; D046911:Macromolecular Substances; D008958:Models, Molecular
D046911:Macromolecular Substances