ICCAS OpenIR
Multiple-Docking and Affinity Fingerprint Methods for Protein Classification and Inhibitors Selection
Li, Bo3; Liu, Zhenming1,2; Zhang, Liangren1; Zhang, Lihe1
2009-07-01
Source PublicationJOURNAL OF CHEMICAL INFORMATION AND MODELING
ISSN1549-9596
Volume49Issue:7Pages:1725-1733
AbstractThe function-based protein classification holds tremendous promise for molecular recognition and the structure-based design process. We describe here a new strategy combined with multiple-docking tools and "affinity fingerprint" analysis technology to detect functional relationships among proteins based on the substrate binding features and protein - ligand interaction matrix and apply it successfully for the family of phospholipase A2 to investigate protein-ligand binding, function-based protein classification, and inhibitor selection, evaluation. Binding data and matrix were generated by multiple versus multiple-docking among 12 PLA2s and 84 PLA2 inhibitors. Three kinds of statistic techniques, principal component analysis, multidimensional scaling, and cluster algorithms, were chosen. to distinguish the groups with similar binding characteristics. The 12 PLA2s were automatically categorized into reasonable subfamilies on the basis of the protein-ligand binding matrix, and the classifying problem of cPLA2 (PDB ID: 1CJY) with relatively low homology was successfully dealt with. This approach was also used to identify and group the selective inhibitors against human nonpancreatic sPLA2. A sound pharmacophore has been defined from these selective inhibitors. It shows that the method is quite robust against individual data deviation, especially false positive, which makes it possible to be used in virtual screening with large enzyme families to generate selective inhibitors of targets on the basis of limited structural/function information.
DOI10.1021/ci900044j
Indexed BySCI
Language英语
WOS IDWOS:000268138900012
PublisherAMER CHEMICAL SOC
Citation statistics
Cited Times:6[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.iccas.ac.cn/handle/121111/66808
Collection中国科学院化学研究所
Corresponding AuthorLiu, Zhenming
Affiliation1.Peking Univ, State Key Lab Nat & Biomimet Drugs, Sch Pharmaceut Sci, Beijing 100191, Peoples R China
2.Peking Univ, Ctr Hlth, Sch Pharmaceut Sci, Beijing 100191, Peoples R China
3.Peking Univ, State Key Lab Struct Chem Unstable & Stable Speci, Coll Chem & Mol Engn, Beijing 100871, Peoples R China
Recommended Citation
GB/T 7714
Li, Bo,Liu, Zhenming,Zhang, Liangren,et al. Multiple-Docking and Affinity Fingerprint Methods for Protein Classification and Inhibitors Selection[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING,2009,49(7):1725-1733.
APA Li, Bo,Liu, Zhenming,Zhang, Liangren,&Zhang, Lihe.(2009).Multiple-Docking and Affinity Fingerprint Methods for Protein Classification and Inhibitors Selection.JOURNAL OF CHEMICAL INFORMATION AND MODELING,49(7),1725-1733.
MLA Li, Bo,et al."Multiple-Docking and Affinity Fingerprint Methods for Protein Classification and Inhibitors Selection".JOURNAL OF CHEMICAL INFORMATION AND MODELING 49.7(2009):1725-1733.
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