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(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.
Bhattacharyay
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Dipartimento di Fisica G.Galilei, Universitá degli Studi di Padova, via F. Marzolo 8, 35131 Padova, Italy. arijit@pd.infn.it
Trovato
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Seno
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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
D000596:Amino Acids; D011506:Proteins; D012997:Solvents