Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function
文献类型：期刊论文
| 作者 | Gu, Junfeng2; Li, Honglin1,3; Jiang, Hualiang1,3 ; Wang, Xicheng2
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| 刊名 | JOURNAL OF COMPUTATIONAL BIOLOGY
 |
| 出版日期 | 2009-03 |
| 卷号 | 16期号:3页码:427-441 |
| 关键词 | parametric evaluation function method potential function protein fold recognition |
| ISSN号 | 1066-5277 |
| DOI | 10.1089/cmb.2008.0128 |
| 文献子类 | Article |
| 英文摘要 | In this paper, a new optimization method is proposed to determine a simplified energy potential for protein fold recognition, which consists of the residue-residue contact, hydrophobicity, and pseudodihedral potentials. With a parametric evaluation function method, the Z-scores of all the proteins in a training set are optimized simultaneously to obtain the best parameter set of the potential. For this multi-objective and multi-constraint problem, the new optimization scheme is very effective. The derived potential is then tested on two high-quality decoy sets and compared with other classical fold recognition potentials. With the simplified energy potential, we achieve a high level of discrimination capability between correct and incorrect folds. |
| WOS关键词 | QUASI-CHEMICAL APPROXIMATION ; STRUCTURE-DERIVED POTENTIALS ; GAS REFERENCE STATE ; STATISTICAL POTENTIALS ; STRUCTURE PREDICTION ; GLOBULAR-PROTEINS ; MEAN FORCE ; PAIR POTENTIALS ; TERTIARY STRUCTURES ; RESIDUE POTENTIALS |
| 资助项目 | National Natural Science Foundation[10572033] ; National Natural Science Foundation[30672539] ; National Natural Science Foundation[20803022] ; National Natural Science Foundation[20721003] ; National Basic Research Program of China[2004CB518901] ; National Basic Research Program of China[2009CB918501] ; 863 Hi-Tech Program of China[2006AA01A124] ; 863 Hi-Tech Program of China[2007AA02Z304] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| 语种 | 英语 |
| WOS记录号 | WOS:000263770200002 |
| 出版者 | MARY ANN LIEBERT, INC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/279303]  |
| 专题 | 药物发现与设计中心 中科院受体结构与功能重点实验室 新药研究国家重点实验室 |
| 通讯作者 | Wang, Xicheng |
| 作者单位 | 1.E China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China 2.Dalian Univ Technol, Dept Engn Mech, State Key Lab Struct Anal Ind Equipment, Dalian 116024, Peoples R China; 3.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Drug Discovery & Design Ctr, Shanghai 200031, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Gu, Junfeng,Li, Honglin,Jiang, Hualiang,et al. Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function[J]. JOURNAL OF COMPUTATIONAL BIOLOGY,2009,16(3):427-441. |
| APA | Gu, Junfeng,Li, Honglin,Jiang, Hualiang,&Wang, Xicheng.(2009).Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function.JOURNAL OF COMPUTATIONAL BIOLOGY,16(3),427-441. |
| MLA | Gu, Junfeng,et al."Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function".JOURNAL OF COMPUTATIONAL BIOLOGY 16.3(2009):427-441. |
入库方式： OAI收割
来源：上海药物研究所
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