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Simple solvation potential for coarse-grained models of proteins

A. Bhattacharyay·A. Trovato·F. Seno
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Abstract

We formulate a simple solvation potential based on a coarsed-grain representation of amino acids with two spheres modeling the $C_α$ 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 neighbours 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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A. Bhattacharyay, A. Trovato, F. Seno. 2006-06-22. Simple solvation potential for coarse-grained models of proteins. https://arxiv.org/abs/q-bio/0606031

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