ITP OpenIR  > 理论物理所科研产出  > SCI论文
Zhang, CX; Mortuza, SM; He, BJ; Wang, YT; Zhang, Y1
Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12
Source PublicationPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Language英语
KeywordPROTEIN-STRUCTURE PREDICTION RESIDUE CONTACTS SEQUENCE ALIGNMENTS ACCURACY NETWORKS ROLL
AbstractWe develop two complementary pipelines, Zhang-Server and QUARK, based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines. The inclusion of NeBcon predicted contacts as restraints in the QUARK simulations results in an average TM-score of 0.41 for the best in top five predicted models, which is 37% higher than that by the QUARK simulations without contacts. In particular, there are seven targets that are converted from non-foldable to foldable (TM-score >0.5) due to the use of contact restraints in the simulations. Another additional feature in the current pipelines is the local structure quality prediction by ResQ, which provides a robust residue-level modeling error estimation. Despite the success, significant challenges still remain in ab initio modeling of multi-domain proteins and folding of -proteins with complicated topologies bound by long-range strand-strand interactions. Improvements on domain boundary and long-range contact prediction, as well as optimal use of the predicted contacts and multiple threading alignments, are critical to address these issues seen in the CASP12 experiment.
2018
ISSN0887-3585
Volume86Pages:136-151
Subject AreaBiochemistry & Molecular Biology ; Biophysics
MOST Discipline CatalogueBiochemistry & Molecular Biology ; Biophysics
DOI10.1002/prot.25414
Indexed BySCIE
Citation statistics
Cited Times:17[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/22950
Collection理论物理所科研产出_SCI论文
Affiliation1.Univ Michigan, Dept Computat Med & Bioinformat, 100 Washtenaw Ave, Ann Arbor, MI 48109 USA
2.Univ Michigan, Dept Biol Chem, Ann Arbor, MI 48109 USA
3.Chinese Acad Sci, Inst Theoret Phys, Beijing, Peoples R China
Recommended Citation
GB/T 7714
Zhang, CX,Mortuza, SM,He, BJ,et al. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2018,86:136-151.
APA Zhang, CX,Mortuza, SM,He, BJ,Wang, YT,&Zhang, Y.(2018).Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,86,136-151.
MLA Zhang, CX,et al."Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 86(2018):136-151.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Zhang, CX]'s Articles
[Mortuza, SM]'s Articles
[He, BJ]'s Articles
Baidu academic
Similar articles in Baidu academic
[Zhang, CX]'s Articles
[Mortuza, SM]'s Articles
[He, BJ]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Zhang, CX]'s Articles
[Mortuza, SM]'s Articles
[He, BJ]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.