dorsal/arxiv
View SchemaConservation of statistical results under the reduction of pair-contact interactions to solvation interactions
| Authors | N. Hamedani Radja, R. R. Farzami, M. R. Ejtehadi |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0511014 |
| URL | https://arxiv.org/abs/q-bio/0511014 |
| DOI | 10.1103/PhysRevE.72.061915 |
| Journal | Phys. Rev. E 72, 061915 (2005) |
Abstract
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically non-degenerate vectors (structures) as protein-like structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of designability-ranking shows that about 1/e of the structures have designabilities above the average, independent on the used model.
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"abstract": "We show that the hydrophobicity of sequences is the leading term in\nMiyazawa-Jernigan interactions. Being the source of additive (solvation) terms\nin pair-contact interactions, they were used to reduce the energy parameters\nwhile resulting in a clear vector manipulation of energy. The reduced\n(additive) potential performs considerably successful in predicting the\nstatistical properties of arbitrary structures. The evaluated designabilities\nof the structures by both models are highly correlated. Suggesting\ngeometrically non-degenerate vectors (structures) as protein-like structures,\nthe additive model is a powerful tool for protein design. Moreover, a crossing\npoint in the log-linear diagram of designability-ranking shows that about 1/e\nof the structures have designabilities above the average, independent on the\nused model.",
"arxiv_id": "q-bio/0511014",
"authors": [
"N. Hamedani Radja",
"R. R. Farzami",
"M. R. Ejtehadi"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"doi": "10.1103/PhysRevE.72.061915",
"journal_ref": "Phys. Rev. E 72, 061915 (2005)",
"title": "Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions",
"url": "https://arxiv.org/abs/q-bio/0511014"
},
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