dorsal/arxiv
View SchemaPotential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry
| Authors | Jinfeng Zhang, Rong Chen, Jie Liang |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0407030 |
| URL | https://arxiv.org/abs/q-bio/0407030 |
| DOI | 10.1109/IEMBS.2004.1403844 |
Abstract
An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is important. Such a simplified model is essential for efficient search of conformational space. In this work, we present a formulation of potential function for simplified representations of protein structures. It is based on the combination of descriptors derived from residue-residue contact and sequence-dependent local geometry. The optimal weight coefficients for contact and local geometry is obtained through optimization by maximizing margins among native and decoy structures. The latter are generated by chain growth and by gapless threading. The performance of the potential function in blind test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. This potential function have comparable or better performance than several residue-based potential functions that require in addition coordinates of side chain centers or coordinates of all side chain atoms.
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"abstract": "An effective potential function is critical for protein structure prediction\nand folding simulation. For simplified models of proteins where coordinates of\nonly $C_\\alpha$ atoms need to be specified, an accurate potential function is\nimportant. Such a simplified model is essential for efficient search of\nconformational space. In this work, we present a formulation of potential\nfunction for simplified representations of protein structures. It is based on\nthe combination of descriptors derived from residue-residue contact and\nsequence-dependent local geometry. The optimal weight coefficients for contact\nand local geometry is obtained through optimization by maximizing margins among\nnative and decoy structures. The latter are generated by chain growth and by\ngapless threading. The performance of the potential function in blind test of\ndiscriminating native protein structures from decoys is evaluated using several\nbenchmark decoy sets. This potential function have comparable or better\nperformance than several residue-based potential functions that require in\naddition coordinates of side chain centers or coordinates of all side chain\natoms.",
"arxiv_id": "q-bio/0407030",
"authors": [
"Jinfeng Zhang",
"Rong Chen",
"Jie Liang"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1109/IEMBS.2004.1403844",
"title": "Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry",
"url": "https://arxiv.org/abs/q-bio/0407030"
},
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