dorsal/arxiv
View SchemaSimple solvation potential for coarse-grained models of proteins
| Authors | A. Bhattacharyay, A. Trovato, F. Seno |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0606031 |
| URL | https://arxiv.org/abs/q-bio/0606031 |
Abstract
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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"abstract": "We formulate a simple solvation potential based on a coarsed-grain\nrepresentation of amino acids with two spheres modeling the $C_\\alpha$ atom and\nan effective side-chain centroid. The potential relies on a new method for\nestimating the buried area of residues, based on counting the effective number\nof burying neighbours in a suitable way. This latter quantity shows a good\ncorrelation with the buried area of residues computed from all atom\ncrystallographic structures. We check the discriminatory power of the solvation\npotential alone to identify the native fold of a protein from a set of decoys\nand show the potential to be considerably selective.",
"arxiv_id": "q-bio/0606031",
"authors": [
"A. Bhattacharyay",
"A. Trovato",
"F. Seno"
],
"categories": [
"q-bio.BM"
],
"title": "Simple solvation potential for coarse-grained models of proteins",
"url": "https://arxiv.org/abs/q-bio/0606031"
},
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