ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)

@article{Warr2009ChEMBLAI,
  title={ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)},
  author={Wendy A. Warr},
  journal={Journal of Computer-Aided Molecular Design},
  year={2009},
  volume={23},
  pages={195-198}
}
  • W. Warr
  • Published 5 February 2009
  • Biology, Chemistry
  • Journal of Computer-Aided Molecular Design
John Overington holds a first degree in chemistry, and studied for his PhD on comparative protein modeling, drug design, and sequence-structure relationships with Sir Tom Blundell FRS, at Birkbeck College, London. After a postdoctoral fellowship with the Imperial Cancer Research Fund, London, he joined Pfizer Central Research in the UK and eventually became manager of the Molecular Informatics, Structure and Design Department, where he was responsible for cheminformatics, structural biology… 

BindingDB and ChEMBL: online compound databases for drug discovery

This editorial highlights two major public domain compound data repositories, BindingDB and ChEMBL, which have different origins and provide a substantial body of complementary compound activity information.

Reactome: a database of reactions, pathways and biological processes

A new web site with improved tools for pathway browsing and data analysis is developed, and orthology-based inferences of pathways in non-human species are made, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species.

Mitigating heterocycle metabolism in drug discovery.

This review summarizes examples where changes were made at or near the heterocycle to improve metabolic stability of heterocycles and hopes to provide a useful guide to medicinal chemists as they attempt to improve the metabolic profile of their own heterocyclic compounds.

SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents

SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases, and is discussed how such information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization.

Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach

This work presents strategies to prioritize pathogen proteins based on whether their properties meet criteria considered desirable in a drug target, based upon both sequence-derived information and functional data on expression, essentiality, phenotypes, metabolic pathways, assayability, and druggability.

Drug target central

Using Pfizer's internal target database as a narrative, this work considers how compiling the drug target universe requires integration across several resources such as competitor intelligence and pharmacological activity databases, as well as input from techniques such as text-mining.

Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening

A strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors with new scaffolds with IC50 values ranging 0.44–31.25 μM is reported.

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

The work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context is described.

ZINClick: A Database of 16 Million Novel, Patentable, and Readily Synthesizable 1, 4-Disubstituted Triazoles

A database of triazoles called ZINClick is generated from literature-reported alkynes and azides that can be synthesized within three steps from commercially available products and contains over 16 million 1,4-disubstituted-1,2,3-triazoles that are easily synthesizable, new, and patentable.

Comparative Analysis of Pharmacophore Screening Tools

A comparative analysis of eight pharmacophore screening algorithms for their use in typical HTVS campaigns against four different biological targets by using default settings provides a valuable benchmark set for further developments in the field of Pharmacophore search algorithms, e.g., by using pose predictions and compound library enrichment criteria.
...

References

SHOWING 1-4 OF 4 REFERENCES

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo-and Bioinformatics

The Chemistry Development Kit provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc.

Genomic-scale prioritization of drug targets: the TDR Targets database

The development of the TDR Targets database is discussed, which encompasses extensive genetic, biochemical and pharmacological data related to tropical disease pathogens, as well as computationally predicted druggability for potential targets and compound desirability information, and aims to facilitate the identification and prioritization of candidate drug targets for pathogens.

Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

The Chemistry Development Kit's new QSAR capabilities and the recently introduced interface to statistical software are introduced.

How many drug targets are there?

A consensus number of current drug targets for all classes of approved therapeutic drugs is proposed, and an emerging realization of the importance of polypharmacology and also the power of a gene-family-led approach in generating novel and important therapies is highlighted.