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PDB-wide collection of binding data: current status of the PDBbind database
Alternative TitlePDB数据库亲和性数据的广泛收集: PDBbind数据库的现状
Liu ZH(刘志海); Li Y(李嫣); Han L(韩莉); Li J(李婕); Liu J(刘杰); Zhao ZX(赵志雄); Nie W(聂伟); Liu YC(刘宇晨); Wang RX(王任小)
2015
Source PublicationBioinformatics
Volume31Issue:3Pages:405-412
AbstractMotivation: Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Results: Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10 776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. Availability and implementation: All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/.
Subtype论文
Subject Area计算机化学
DOI10.1093/bioinformatics/btu626
URL查看原文
Indexed BySCI
Language英语
WOS IDWOS:000350058800015
Citation statistics
Cited Times:76[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.sioc.ac.cn/handle/331003/39820
Collection计算机化学与化学信息学研究室
Corresponding AuthorWang RX(王任小)
Affiliation中科院上海有机化学研究所
Recommended Citation
GB/T 7714
Liu ZH,Li Y,Han L,et al. PDB-wide collection of binding data: current status of the PDBbind database[J]. Bioinformatics,2015,31(3):405-412.
APA 刘志海.,李嫣.,韩莉.,李婕.,刘杰.,...&王任小.(2015).PDB-wide collection of binding data: current status of the PDBbind database.Bioinformatics,31(3),405-412.
MLA 刘志海,et al."PDB-wide collection of binding data: current status of the PDBbind database".Bioinformatics 31.3(2015):405-412.
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