SIOC OpenIR  > 计算机化学与化学信息学研究室
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
Source PublicationMol. Inf.
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.
Subject Area计算机化学
Indexed BySCI
WOS IDWOS:000359920700006
Citation statistics
Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
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
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.
Files in This Item:
File Name/Size DocType Version Access License
2015439.pdf(922KB)期刊论文作者接受稿开放获取CC BY-NC-SAApplication Full Text
Related Services
Recommend this item
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[刘志海]'s Articles
[李婕]'s Articles
[刘杰]'s Articles
Baidu academic
Similar articles in Baidu academic
[刘志海]'s Articles
[李婕]'s Articles
[刘杰]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[刘志海]'s Articles
[李婕]'s Articles
[刘杰]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.