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Cross-Mapping of Protein - Ligand Binding Data Between ChEMBL and PDBbind
Alternative TitleChEMBL和PDBbind数据库中的配体-受体亲和数据的相互关系
Liu ZH(刘志海)1; Li J(李婕)1; Liu J(刘杰)1; Liu YC(刘宇晨)1; Nie W(聂伟)1; Han L(韩莉)1; Li Y(李嫣)1; Wang RX(王任小)1
2015
Source PublicationMol. Inf.
Volume34Issue:8Pages:568-576
AbstractThe ChEMBL database is a valuable open data source, which provides a comprehensive collection of binding data, functional and ADMET properties of bioactive compounds. The PDBbind database has a more focused scope, i.e. collecting binding data for the protein-ligand complexes in the Protein Data Bank. Currently, the PDBbind collection of binding data is rather modest as compared to the ChEMBL collection (approximate to 13000 versus approximate to 1.3 million). One may suspect if the former is actually a subset of the latter. In this study, we mapped the molecular information and protein-ligand binding data in PDBbind to the records in ChEMBL, and then analyzed the overlap between the binding data recorded in these two databases. Our results indicate that only approximate to 20% of the binding data in PDBbind can find their counterparts in ChEMBL. Thus, the PDBbind collection of binding data is largely complementary to the ChEMBL collection. We also reveal two reasons accounting for the low overlap between two databases: First, only a minor fraction of the protein-ligand complexes in PDBbind is covered by ChEMBL; Second, the literature spaces screened by these two databases do not have a substantial overlap either. The value of focused databases versus more comprehensive ones is demonstrated by our study.
Subtype论文
Subject Area计算机化学
DOI10.1002/minf.201500010
URL查看原文
Indexed BySCI
Language英语
WOS IDWOS:000359920700006
Citation statistics
Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.sioc.ac.cn/handle/331003/39823
Collection计算机化学与化学信息学研究室
Corresponding AuthorWang RX(王任小)
Affiliation1.中科院上海有机化学研究所, 生命有机化学国家重点实验室
2.澳门科技大学
Recommended Citation
GB/T 7714
Liu ZH,Li J,Liu J,et al. Cross-Mapping of Protein - Ligand Binding Data Between ChEMBL and PDBbind[J]. Mol. Inf.,2015,34(8):568-576.
APA 刘志海.,李婕.,刘杰.,刘宇晨.,聂伟.,...&王任小.(2015).Cross-Mapping of Protein - Ligand Binding Data Between ChEMBL and PDBbind.Mol. Inf.,34(8),568-576.
MLA 刘志海,et al."Cross-Mapping of Protein - Ligand Binding Data Between ChEMBL and PDBbind".Mol. Inf. 34.8(2015):568-576.
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