BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server
文献类型：期刊论文
| 作者 | Xiong, Bing3 ; Wu, Jie2; Burk, David L.1; Xue, Mengzhu3; Jiang, Hualiang3; Shen, Jingkang3
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| 刊名 | BMC BIOINFORMATICS
 |
| 出版日期 | 2010-01-25 |
| 卷号 | 11 |
| ISSN号 | 1471-2105 |
| DOI | 10.1186/1471-2105-11-47 |
| 文献子类 | Article |
| 英文摘要 | Background: Genome sequencing and post-genomics projects such as structural genomics are extending the frontier of the study of sequence-structure-function relationship of genes and their products. Although many sequence/structure-based methods have been devised with the aim of deciphering this delicate relationship, there still remain large gaps in this fundamental problem, which continuously drives researchers to develop novel methods to extract relevant information from sequences and structures and to infer the functions of newly identified genes by genomics technology. Results: Here we present an ultrafast method, named BSSF(Binding Site Similarity & Function), which enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. After conducting the database searching, the hit list is further analyzed to provide basic statistical information about the occurrences of Gene Ontology terms and Enzyme Commission numbers, which may benefit researchers by helping them to design further experiments to study the query proteins. Conclusions: This ultrafast web-based system will not only help researchers interested in drug design and structural genomics to identify similar binding sites, but also assist them by providing further analysis of hit list from database searching. |
| WOS关键词 | PROTEIN FUNCTION PREDICTION ; SIDE-CHAIN PATTERNS ; STRUCTURAL GENOMICS ; SEQUENCE ; RECOGNITION ; DATABASE ; FOLD ; CLASSIFICATION ; INFORMATION ; TEMPLATES |
| 资助项目 | National Natural Science Foundation of China[30600784] ; State Key Program of Basic Research of China[009CB918502] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000275199700002 |
| 出版者 | BIOMED CENTRAL LTD |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/278990]  |
| 专题 | 药物化学研究室 中科院受体结构与功能重点实验室 新药研究国家重点实验室 |
| 通讯作者 | Xiong, Bing |
| 作者单位 | 1.McGill Univ, Dept Biochem, Montreal, PQ H3A 1A4, Canada 2.SUNY Stony Brook, Dept Appl Math & Stat, Stony Brook, NY 11794 USA; 3.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Shanghai 201203, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Xiong, Bing,Wu, Jie,Burk, David L.,et al. BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server[J]. BMC BIOINFORMATICS,2010,11. |
| APA | Xiong, Bing,Wu, Jie,Burk, David L.,Xue, Mengzhu,Jiang, Hualiang,&Shen, Jingkang.(2010).BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server.BMC BIOINFORMATICS,11. |
| MLA | Xiong, Bing,et al."BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server".BMC BIOINFORMATICS 11(2010). |
入库方式： OAI收割
来源：上海药物研究所
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