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EnglishWe 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.
| Titolo: | Simple solvation potential for coarse-grained models of proteins |
| Autori: | |
| Data di pubblicazione: | 2007 |
| Rivista: | |
| 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. |
| Handle: | http://hdl.handle.net/11577/2437845 |
| Appare nelle tipologie: | 01.01 - Articolo in rivista |
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