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  • Title: Simple solvation potential for coarse-grained models of proteins.
    Author: Bhattacharyay A, Trovato A, Seno F.
    Journal: Proteins; 2007 May 01; 67(2):285-92. PubMed ID: 17286285.
    Abstract:
    We formulate a simple solvation potential based on a coarsed-grained representation of amino acids with two spheres modeling the C(alpha) atom and an effective side-chain centroid. The potential relies on a new method for estimating the buried area of residues, based on counting the effective number of burying neighbors in a suitable way. This latter quantity shows a good correlation with the buried area of residues computed from all atom crystallographic structures. We check the discriminatory power of the solvation potential alone to identify the native fold of a protein from a set of decoys and show the potential to be considerably selective.
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