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
发表期刊PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
语种英语
关键词PROTEIN-STRUCTURE PREDICTION RESIDUE CONTACTS SEQUENCE ALIGNMENTS ACCURACY NETWORKS ROLL
摘要We 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
卷号86页码:136-151
学科领域Biochemistry & Molecular Biology ; Biophysics
学科门类Biochemistry & Molecular Biology ; Biophysics
DOI10.1002/prot.25414
收录类别SCIE
引用统计
被引频次:9[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/22950
专题理论物理所科研产出_SCI论文
作者单位1.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
推荐引用方式
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.
条目包含的文件
条目无相关文件。
个性服务
推荐该条目
保存到收藏夹
查看访问统计
导出为Endnote文件
谷歌学术
谷歌学术中相似的文章
[Zhang, CX]的文章
[Mortuza, SM]的文章
[He, BJ]的文章
百度学术
百度学术中相似的文章
[Zhang, CX]的文章
[Mortuza, SM]的文章
[He, BJ]的文章
必应学术
必应学术中相似的文章
[Zhang, CX]的文章
[Mortuza, SM]的文章
[He, BJ]的文章
相关权益政策
暂无数据
收藏/分享
所有评论 (0)
暂无评论
 

除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。