dorsal/arxiv
View SchemaHigh resolution protein folding with a transferable potential
| Authors | Isaac A. Hubner, Eric J. Deeds, Eugene I. Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0509007 |
| URL | https://arxiv.org/abs/q-bio/0509007 |
| DOI | 10.1073/pnas.0502181102 |
Abstract
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systematically applied and consistently produced structure predictions of approximately 3 Angstroms without any knowledge of the native state. To measure and understand the significance of the results, extensive control simulations were conducted. Graph theoretic analysis provides a means for systematically identifying the native fold and provides physical insight, conceptually linking the results to modern theoretical views of protein folding. In addition to presenting a method for prediction of structure and folding mechanism, our model suggests that a accurate all-atom amino acid representation coupled with a physically reasonable atomic interaction potential (that does not require optimization to the test set) and hydrogen bonding are essential features for a realistic protein model.
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"abstract": "A generalized computational method for folding proteins with a fully\ntransferable potential and geometrically realistic all-atom model is presented\nand tested on seven different helix bundle proteins. The protocol, which\nincludes graph-theoretical analysis of the ensemble of resulting folded\nconformations, was systematically applied and consistently produced structure\npredictions of approximately 3 Angstroms without any knowledge of the native\nstate. To measure and understand the significance of the results, extensive\ncontrol simulations were conducted. Graph theoretic analysis provides a means\nfor systematically identifying the native fold and provides physical insight,\nconceptually linking the results to modern theoretical views of protein\nfolding. In addition to presenting a method for prediction of structure and\nfolding mechanism, our model suggests that a accurate all-atom amino acid\nrepresentation coupled with a physically reasonable atomic interaction\npotential (that does not require optimization to the test set) and hydrogen\nbonding are essential features for a realistic protein model.",
"arxiv_id": "q-bio/0509007",
"authors": [
"Isaac A. Hubner",
"Eric J. Deeds",
"Eugene I. Shakhnovich"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1073/pnas.0502181102",
"title": "High resolution protein folding with a transferable potential",
"url": "https://arxiv.org/abs/q-bio/0509007"
},
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"type": "Model",
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