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Faraggi, E1; Krupa, P3; Mozolewska, MA; Liwo, A5,6,7; Kloczkowski, A2,8,9,10
Reoptimized UNRES Potential for Protein Model Quality Assessment
Source PublicationGENES
Language英语
KeywordRESIDUE FORCE-FIELD KNOWLEDGE-BASED POTENTIALS ACCESSIBLE SURFACE-AREA STRUCTURE PREDICTION MOLECULAR-DYNAMICS STATISTICAL POTENTIALS STRUCTURE SIMULATIONS POLYPEPTIDE-CHAINS SCORING FUNCTION WEB SERVER
AbstractRanking 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.
2018
ISSN2073-4425
Volume9Issue:12Pages:601
Subject AreaGenetics & Heredity
MOST Discipline CatalogueGenetics & Heredity
DOI10.3390/genes9120601
Indexed BySCIE
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/23532
CollectionSCI期刊论文
Affiliation1.Res & Informat Syst LLC, Indianapolis, IN 46240 USA
2.Indiana Univ Purdue Univ, Dept Phys, Indianapolis, IN 46202 USA
3.Nationwide Childrens Hosp, Battelle Ctr Math Med, Columbus, OH 43215 USA
4.Polish Acad Sci, Inst Phys, Al Lotnikow 32-46, PL-02668 Warsaw, Poland
5.Mozolewska, Magdalena A.] Polish Acad Sci, Inst Comp Sci, Ul Jana Kazimierza 5, PL-01248 Warsaw, Poland
6.Univ Gdansk, Fac Chem, Wita Stwosza 63, PL-80308 Gdansk, Poland
7.Korea Inst Adv Study, Ctr In Silico Prot Struct, 85 Hoegiro, Seoul 130722, South Korea
8.Korea Inst Adv Study, Sch Computat Sci, 85 Hoegiro, Seoul 130722, South Korea
9.Ohio State Univ, Dept Pediat, Columbus, OH 43215 USA
10.Chinese Acad Sci, Kavli Inst Theoret Phys China, Beijing 100190, Peoples R China
11.Nagoya Univ, Grad Sch Informat, Future Value Creat Res Ctr, Nagoya, Aichi 4648601, Japan
Recommended Citation
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.
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