Reoptimized UNRES Potential for Protein Model Quality Assessment

doi:10.3390/genes9120601

CORC > 理论物理研究所 > 中国科学院理论物理研究所 > 理论物理所科研产出 > 理论物理所1978-2010年知识产出

	Reoptimized UNRES Potential for Protein Model Quality Assessment
	Faraggi, E 11; Krupa, P 4; Mozolewska, MA ; Liwo, A 6,7,8; Kloczkowski, A 1,3,9,10
刊名	GENES
	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
内容类型	期刊论文
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.Ohio State Univ, Dept Pediat, Columbus, OH 43215 USA 2.Nagoya Univ, Grad Sch Informat, Future Value Creat Res Ctr, Nagoya, Aichi 4648601, Japan 3.Indiana Univ Purdue Univ, Dept Phys, Indianapolis, IN 46202 USA 4.Nationwide Childrens Hosp, Battelle Ctr Math Med, Columbus, OH 43215 USA 5.Polish Acad Sci, Inst Phys, Al Lotnikow 32-46, PL-02668 Warsaw, Poland 6.Mozolewska, Magdalena A.] Polish Acad Sci, Inst Comp Sci, Ul Jana Kazimierza 5, PL-01248 Warsaw, Poland 7.Univ Gdansk, Fac Chem, Wita Stwosza 63, PL-80308 Gdansk, Poland 8.Korea Inst Adv Study, Ctr In Silico Prot Struct, 85 Hoegiro, Seoul 130722, South Korea 9.Korea Inst Adv Study, Sch Computat Sci, 85 Hoegiro, Seoul 130722, South Korea 10.Chinese Acad Sci, Kavli Inst Theoret Phys China, Beijing 100190, Peoples R China
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.