Reoptimized UNRES Potential for Protein Model Quality Assessment
文献类型：期刊论文
| 作者 | Faraggi, E4; Krupa, P6; Mozolewska, MA; Liwo, A8,9,10; Kloczkowski, A1,2,3,5 |
| 刊名 | GENES
 |
| 出版日期 | 2018 |
| 卷号 | 9期号:12页码:601 |
| 关键词 | RESIDUE FORCE-FIELD KNOWLEDGE-BASED POTENTIALS ACCESSIBLE SURFACE-AREA STRUCTURE PREDICTION MOLECULAR-DYNAMICS STATISTICAL POTENTIALS STRUCTURE SIMULATIONS POLYPEPTIDE-CHAINS SCORING FUNCTION WEB SERVER |
| ISSN号 | 2073-4425 |
| DOI | 10.3390/genes9120601 |
| 英文摘要 | Ranking protein structure models is an elusive problem in bioinformatics. These models are evaluated on both the degree of similarity to the native structure and the folding pathway. Here, we simulated the use of the coarse-grained UNited RESidue (UNRES) force field as a tool to choose the best protein structure models for a given protein sequence among a pool of candidate models, using server data from the CASP11 experiment. Because the original UNRES was optimized for Molecular Dynamics simulations, we reoptimized UNRES using a deep feed-forward neural network, and we show that introducing additional descriptive features can produce better results. Overall, we found that the reoptimized UNRES performs better in selecting the best structures and tracking protein unwinding from its native state. We also found a relatively poor correlation between UNRES values and the model's Template Modeling Score (TMS). This is remedied by reoptimization. We discuss some cases where our reoptimization procedure is useful. |
| 学科主题 | Genetics & Heredity |
| 语种 | 英语 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/23532]  |
| 专题 | 理论物理研究所_理论物理所1978-2010年知识产出 |
| 作者单位 | 1.Chinese Acad Sci, Kavli Inst Theoret Phys China, Beijing 100190, Peoples R China 2.Ohio State Univ, Dept Pediat, Columbus, OH 43215 USA 3.Korea Inst Adv Study, Sch Computat Sci, 85 Hoegiro, Seoul 130722, South Korea 4.Res & Informat Syst LLC, Indianapolis, IN 46240 USA 5.Indiana Univ Purdue Univ, Dept Phys, Indianapolis, IN 46202 USA 6.Nationwide Childrens Hosp, Battelle Ctr Math Med, Columbus, OH 43215 USA 7.Polish Acad Sci, Inst Phys, Al Lotnikow 32-46, PL-02668 Warsaw, Poland 8.Mozolewska, Magdalena A.] Polish Acad Sci, Inst Comp Sci, Ul Jana Kazimierza 5, PL-01248 Warsaw, Poland 9.Korea Inst Adv Study, Ctr In Silico Prot Struct, 85 Hoegiro, Seoul 130722, South Korea 10.Univ Gdansk, Fac Chem, Wita Stwosza 63, PL-80308 Gdansk, Poland |
| 推荐引用方式 GB/T 7714 | Faraggi, E,Krupa, P,Mozolewska, MA,et al. Reoptimized UNRES Potential for Protein Model Quality Assessment[J]. GENES,2018,9(12):601. |
| APA | Faraggi, E,Krupa, P,Mozolewska, MA,Liwo, A,&Kloczkowski, A.(2018).Reoptimized UNRES Potential for Protein Model Quality Assessment.GENES,9(12),601. |
| MLA | Faraggi, E,et al."Reoptimized UNRES Potential for Protein Model Quality Assessment".GENES 9.12(2018):601. |
入库方式： OAI收割
来源：理论物理研究所
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