Physics-Based Modeling of Side Chain - Side Chain Interactions in the UNRES Force Field

Part of the Springer Series in Bio-/Neuroinformatics book series (SSBN, volume 1)

Abstract

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.

Keywords

amino acid side chains model of side-chain – side-chain interactions potential of mean force hydrophobic interactions temperature dependence molecular dynamics umbrella sampling 

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© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Faculty of ChemistryUniversity of GdańskGdańskPoland

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