Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins
文献类型：期刊论文
| 作者 | Li, Chen1; Chang, Catherine Ching Han2; Nagel, Jeremy; Porebski, Benjamin T.3; Hayashida, Morihiro4; Akutsu, Tatsuya4; Song, Jiangning5,6; Buckle, Ashley M.3 |
| 刊名 | BRIEFINGS IN BIOINFORMATICS
 |
| 出版日期 | 2016-03-01 |
| 卷号 | 17期号:2页码:270-282 |
| 关键词 | coiled-coil prediction oligomeric state polyglutamine |
| 英文摘要 | Coiled-coils refer to a bundle of helices coiled together like strands of a rope. It has been estimated that nearly 3% of protein-encoding regions of genes harbour coiled-coil domains (CCDs). Experimental studies have confirmed that CCDs play a fundamental role in subcellular infrastructure and controlling trafficking of eukaryotic cells. Given the importance of coiled-coils, multiple bioinformatics tools have been developed to facilitate the systematic and high-throughput prediction of CCDs in proteins. In this article, we review and compare 12 sequence-based bioinformatics approaches and tools for coiled-coil prediction. These approaches can be categorized into two classes: coiled-coil detection and coiled-coil oligomeric state prediction. We evaluated and compared these methods in terms of their input/output, algorithm, prediction performance, validation methods and software utility. All the independent testing data sets are available at ext-link-type="uri" xlink:href="http://lightning.med.monash.edu/coiledcoil/">http://lightning.med.monash.edu/coiledcoil/. In addition, we conducted a case study of nine human polyglutamine (PolyQ) disease-related proteins and predicted CCDs and oligomeric states using various predictors. Prediction results for CCDs were highly variable among different predictors. Only two peptides from two proteins were confirmed to be CCDs by majority voting. Both domains were predicted to form dimeric coiled-coils using oligomeric state prediction. We anticipate that this comprehensive analysis will be an insightful resource for structural biologists with limited prior experience in bioinformatics tools, and for bioinformaticians who are interested in designing novel approaches for coiled-coil and its oligomeric state prediction. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemical Research Methods ; Mathematical & Computational Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Mathematical & Computational Biology |
| 关键词[WOS] | SPINOCEREBELLAR ATAXIA TYPE-2 ; OLIGOMERIC MATRIX PROTEIN ; TATA-BINDING PROTEIN ; CAG REPEAT EXPANSION ; POLYGLUTAMINE EXPANSIONS ; CRYSTAL-STRUCTURE ; CACNA1A GENE ; EARLY-ONSET ; DATABASE ; CLONING |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000372974300011 |
| 源URL | [http://124.16.173.210/handle/834782/2238]  |
| 专题 | 天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室 宋江宁_期刊论文 |
| 作者单位 | 1.Monash Univ, Dept Biochem & Mol Biol, Fac Med, Clayton, Vic 3800, Australia 2.Monash Univ, Sch Engn, Chem Engn Discipline, Chem Engn, Kuala Lumpur, Malaysia 3.Monash Univ, Dept Biochem & Mol Biol, Melbourne, Vic 3800, Australia 4.Kyoto Univ, Bioinformat Ctr, Inst Chem Res, Kyoto 6068501, Japan 5.Monash Univ, Monash Bioinformat Platform, Fac Med, Melbourne, Vic 3800, Australia 6.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Beijing 100864, Peoples R China |
| 推荐引用方式 GB/T 7714 | Li, Chen,Chang, Catherine Ching Han,Nagel, Jeremy,et al. Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins[J]. BRIEFINGS IN BIOINFORMATICS,2016,17(2):270-282. |
| APA | Li, Chen.,Chang, Catherine Ching Han.,Nagel, Jeremy.,Porebski, Benjamin T..,Hayashida, Morihiro.,...&Buckle, Ashley M..(2016).Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins.BRIEFINGS IN BIOINFORMATICS,17(2),270-282. |
| MLA | Li, Chen,et al."Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins".BRIEFINGS IN BIOINFORMATICS 17.2(2016):270-282. |
入库方式： OAI收割
来源：天津工业生物技术研究所
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