Simple solvation potential for coarse‐grained models of proteins

We formulate a simple solvation potential based on a coarsed‐grained 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 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. Proteins 2007. © 2007 Wiley‐Liss, Inc.