Knowledge Management System of Institute of Theoretical Physics, CAS
Zhang, CX; Mortuza, SM; He, BJ; Wang, YT ; Zhang, Y1
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| Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12 | |
| Source Publication | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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| Language | 英语 |
| Keyword | PROTEIN-STRUCTURE PREDICTION RESIDUE CONTACTS SEQUENCE ALIGNMENTS ACCURACY NETWORKS ROLL |
| Abstract | 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 | |
| ISSN | 0887-3585 |
| Volume | 86Pages:136-151 |
| Subject Area | Biochemistry & Molecular Biology ; Biophysics |
| MOST Discipline Catalogue | Biochemistry & Molecular Biology ; Biophysics |
| DOI | 10.1002/prot.25414 |
| Indexed By | SCIE |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.itp.ac.cn/handle/311006/22950 |
| Collection | SCI期刊论文 |
| Affiliation | 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 |
| 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: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| Template-based and f（2416KB） | 期刊论文 | 作者接受稿 | 开放获取 | CC BY-NC-SA | Application Full Text | |
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