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Erschienen in:
2014 | OriginalPaper | Buchkapitel
Physics-Based Modeling of Side Chain - Side Chain Interactions in the UNRES Force Field
verfasst von : Mariusz Makowski
Erschienen in: Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Verlag: Springer Berlin Heidelberg
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Work on a development of a new model of side-chain – side-chain interactions of amino acids, to be used in the UNRES force-field and in other largescale simulations, has been described in this chapter. In the presented model a polar/charged side chain consists of two interaction sites, ie., nonpolar and polar. General expressions for the effective energy of interaction between amino acids are given depending on the kind of interacting pair. The results of the studies on the influence of particle size on the free-energy profile of hydrophobic interactions, and the temperature dependence of the potential of mean force for side chain – side chain interactions are also presented.