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Predicting gene ontology functions from protein's regional surface structures
Liu, Zhi-Ping1,2; Wu, Ling-Yun1; Wang, Yong1; Chen, Luonan3,4,5,6; Zhang, Xiang-Sun1
2007-12-11
Source PublicationBMC BIOINFORMATICS
ISSN1471-2105
Volume8Pages:13
AbstractBackground: 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.
DOI10.1186/1471-2105-8-475
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS IDWOS:000252973100001
PublisherBIOMED CENTRAL LTD
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/4144
Collection应用数学研究所
Corresponding AuthorWu, Ling-Yun
Affiliation1.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
Recommended Citation
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.
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