dorsal/arxiv
View SchemaAnisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures
| Authors | N. -V. Buchete, J. E. Straub, D. Thirumalai |
|---|---|
| Categories | |
| ArXiv ID | physics/0302009 |
| URL | https://arxiv.org/abs/physics/0302009 |
| DOI | 10.1063/1.1561616 |
| Journal | J. Chem. Phys. 118, 7658-7671 (2003) |
Abstract
We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions is first established by computing orientational order parameters for proteins with alpha-helical and beta-sheet architecture. Extraction of the anisotropic interactions requires defining local reference frames for each amino acid that uniquely determine the coordinates of the neighboring residues. Using the local reference frames and histograms of the radial and angular correlation functions for a standard set of non-homologue protein structures, we construct the anisotropic pair potentials. The performance of the orientation dependent potentials was studied using a large database of decoy proteins. The results demonstrate that the new distance and orientation dependent residue-residue potentials present a significantly improved ability to recognize native folds from a set of native and decoy protein structures.
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"abstract": "We present a new method to extract distance and orientation dependent\npotentials between amino acid side chains using a database of protein\nstructures and the standard Boltzmann device. The importance of orientation\ndependent interactions is first established by computing orientational order\nparameters for proteins with alpha-helical and beta-sheet architecture.\nExtraction of the anisotropic interactions requires defining local reference\nframes for each amino acid that uniquely determine the coordinates of the\nneighboring residues. Using the local reference frames and histograms of the\nradial and angular correlation functions for a standard set of non-homologue\nprotein structures, we construct the anisotropic pair potentials. The\nperformance of the orientation dependent potentials was studied using a large\ndatabase of decoy proteins. The results demonstrate that the new distance and\norientation dependent residue-residue potentials present a significantly\nimproved ability to recognize native folds from a set of native and decoy\nprotein structures.",
"arxiv_id": "physics/0302009",
"authors": [
"N. -V. Buchete",
"J. E. Straub",
"D. Thirumalai"
],
"categories": [
"physics.chem-ph",
"cond-mat.stat-mech",
"physics.bio-ph",
"physics.comp-ph",
"q-bio.BM"
],
"doi": "10.1063/1.1561616",
"journal_ref": "J. Chem. Phys. 118, 7658-7671 (2003)",
"title": "Anisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures",
"url": "https://arxiv.org/abs/physics/0302009"
},
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