Simple solvation potential for coarse-grained models of proteins

Details Simple solvation potential for coarse-grained models of proteins Simple solvation potential for coarse-grained models of proteins

2006-06-22

arxiv.org/abs/q-bio/0606031v1

Biology

Quantitative Biology

Biomolecules

18 pages, 8 tables, 3 figures

Scientific paper

We formulate a simple solvation potential based on a coarsed-grain 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 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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