Predicting gene ontology functions from protein's regional surface structures
文献类型：期刊论文
| 作者 | Liu, Zhi-Ping1,2; Wu, Ling-Yun1 ; Wang, Yong1; Chen, Luonan3,4,5,6; Zhang, Xiang-Sun1
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| 刊名 | BMC BIOINFORMATICS
 |
| 出版日期 | 2007-12-11 |
| 卷号 | 8页码:13 |
| ISSN号 | 1471-2105 |
| DOI | 10.1186/1471-2105-8-475 |
| 英文摘要 | Background: Annotation of protein functions is an important task in the post-genomic era. Most early approaches for this task exploit only the sequence or global structure information. However, protein surfaces are believed to be crucial to protein functions because they are the main interfaces to facilitate biological interactions. Recently, several databases related to structural surfaces, such as pockets and cavities, have been constructed with a comprehensive library of identified surface structures. For example, CAST(P) provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities. Results: A novel method was proposed to predict the Gene Ontology (GO) functions of proteins from the pocket similarity network, which is constructed according to the structure similarities of pockets. The statistics of the networks were presented to explore the relationship between the similar pockets and GO functions of proteins. Cross-validation experiments were conducted to evaluate the performance of the proposed method. Results and codes are available at: http:// zhangroup.aporc.org/bioinfo/PSN/. Conclusion: The computational results demonstrate that the proposed method based on the pocket similarity network is effective and efficient for predicting GO functions of proteins in terms of both computational complexity and prediction accuracy. The proposed method revealed strong relationship between small surface patterns (or pockets) and GO functions, which can be further used to identify active sites or functional motifs. The high quality performance of the prediction method together with the statistics also indicates that pockets play essential roles in biological interactions or the GO functions. Moreover, in addition to pockets, the proposed network framework can also be used for adopting other protein spatial surface patterns to predict the protein functions. |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
| 语种 | 英语 |
| 出版者 | BIOMED CENTRAL LTD |
| WOS记录号 | WOS:000252973100001 |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/4143]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Wu, Ling-Yun |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 2.Grad Univ, Chinese Acad Sci, Beijing 100049, Peoples R China 3.Osaka Sangyo Univ, Dept Elect Informat & Commun Engn, Osaka 5748530, Japan 4.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China 5.JST, ERATO, Aihara Complex Modelling Project, Tokyo 1510064, Japan 6.Univ Tokyo, Inst Ind Sci, Tokyo 1538505, Japan |
| 推荐引用方式 GB/T 7714 | Liu, Zhi-Ping,Wu, Ling-Yun,Wang, Yong,et al. Predicting gene ontology functions from protein's regional surface structures[J]. BMC BIOINFORMATICS,2007,8:13. |
| APA | Liu, Zhi-Ping,Wu, Ling-Yun,Wang, Yong,Chen, Luonan,&Zhang, Xiang-Sun.(2007).Predicting gene ontology functions from protein's regional surface structures.BMC BIOINFORMATICS,8,13. |
| MLA | Liu, Zhi-Ping,et al."Predicting gene ontology functions from protein's regional surface structures".BMC BIOINFORMATICS 8(2007):13. |
入库方式： OAI收割
来源：数学与系统科学研究院
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