ChEMBL database

ChEMBL Group (2010) ChEMBL Database, EMBL-EBl, Cambridge, UK. 

For example, see the ChEMBL database http //www.ebi.ac.uk/chembl/. This public repository of bioactive small molecules, contains 2D structures, calculated properties (e.g., logP, molecular weight, Lipinski parameters, etc.) and abstracted bioactivities (e.g., binding constants, pharmacology, and ADMET data). The data, its maintenance and support is funded by the Wellcome Trust. In the case of singletons, screen hits with no structurally related analogs, these will require further exploration by SAR-by-synthesis for appropriate assessment. 

A virtual libraiy of 150 million antipsychotic molecules of 2 GB file size was generated from four seed scaffolds using the ChemScreener program which is currently not possible with the existing software. It could also reveal significant bioactivity data patterns from scaffold extraction in big databases like PubChem[75] and ChEMBL [76], (Fig. 2.29). 

For example, ChEMBL table in Iporlal database is created with bioactivity data and needs to be accessed via portlet. 

Before going any further, we need to build database entities and services related to them for its working by using Service Builder, a special tool provided by Liferay. To define our entity based on the ChEMBL table stmcture, we create a service.xml file at with the following content. 

Gaulton, A.. Beilis. L.J.. Bento. A.P.. Chambers,)., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., and Overington, J.P. (2011) ChEMBL a large-scale bioactivity database for drug discovery. Nucleic Acids Research, 40, 1-8. 

In order to define compound (activity) classes as input for any computational models, and NBM in particular, compounds, as well as their annotations, need to be standardized. This is particularly important when more than one database is utilized, for example, external databases like ChEMBL, DrugBank, and GVKBio together with internal, proprietary data. In our experience, the following standards and normalization procedures proved useful. 

This entire concept was extended by mining [40, 41] public databases such as BindingDB [42], PubChem [43], or ChEMBL [44]. In such a study, all human target protein pairs were extracted, which share at least five active compounds [40]. This selectivity-centric analysis of protein-ligand data unveils more than 200 scaffolds that appear to be selective for certain target families. A subset of these scaffolds refers to highly selective molecules compared to neighboring proteins [40]. 

Gaulton A, Beilis LJ, Bento AP, et al. ChEMBL A large-scale hioactivity database for dmg discovery. Nucleic Acids Res 2012 40 D1100-D1107. 

Project information describing hypotheses, where compounds are at in a project and decisions made with respect to templates and particular compounds Miscellaneous special purpose databases (e.g., ACD, GeneGo, ChEMBL, custom databases of hterature data built under contract, external chemistry synthesis tracking database, a high throughput reagent database)... 

Bento, A.P., Gaulton, A., Hersey, A. et al (2014) The ChEMBL bioactivity database an update. Nucleic Acids Research, 42, 1083-1090. 

Fig. 2.1 Property histograms of fragrance and taste databases in comparison to ChEMBL, ZINC and GDB-13...

A number of food phytochemicals and food-related molecular databases are available [21], Food and food-related databases are described in more detail in Chap. 9 of this book. Major examples of public databases of chemical compounds annotated with biological activity for dmg-discoveiy apphcations have been developed. Prominent examples include BindingDB, ChEMBL, PubChem, and WOrld of Molecular BioAcTivity (WOMBAT). These databases and others described in Chap. 9 can be analyzed and compared for knowledge of chemical space coverage and potential repurposing, for example, using the concept of similarity searching. 

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