title: Simple solvation potential for coarse-grained models of proteins.
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.
authors.affiliation: Dipartimento di Fisica G.Galilei, Universitá degli Studi di Padova, via F. Marzolo 8, 35131 Padova, Italy. arijit@pd.infn.it
authors.forename: A
authors.initials: A
authors.lastname: Bhattacharyay
authors.forename: A
authors.initials: A
authors.lastname: Trovato
authors.forename: F
authors.initials: F
authors.lastname: Seno
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D018360:Crystallography, X-Ray; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents