Chemical databases: curation or integration by user-defined equivalence?

Anne Hersey,Jon Chambers,Louisa Bellis,A Patrícia Bento,Anna Gaulton,John P Overington

doi:10.1016/j.ddtec.2015.01.005

Anne Hersey, Jon Chambers + Show 4 more

Open Access

https://doi.org/10.1016/j.ddtec.2015.01.005

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Abstract

There is a wealth of valuable chemical information in publicly available databases for use by scientists undertaking drug discovery. However finite curation resource, limitations of chemical structure software and differences in individual database applications mean that exact chemical structure equivalence between databases is unlikely to ever be a reality. The ability to identify compound equivalence has been made significantly easier by the use of the International Chemical Identifier (InChI), a non-proprietary line-notation for describing a chemical structure. More importantly, advances in methods to identify compounds that are the same at various levels of similarity, such as those containing the same parent component or having the same connectivity, are now enabling related compounds to be linked between databases where the structure matches are not exact.

Highlights

Due to the pressures in the pharmaceutical industry of increasing drug development costs, greater requirements for safer medicines and desire for prescribers to show value for money, over the last 5-10 years the industry has changed such that increasingly early drug discovery is being undertaken by SMEs (small to medium sized enterprises) and in academic groups
Due to the pressures in the pharmaceutical industry of increasing drug development costs, greater requirements for safer medicines and desire for prescribers to show value for money, over the last 5-10 years the industry has changed such that increasingly early drug discovery is being undertaken by SMEs and in academic groups
This paper will outline some of the valuable resources available to drug discovery researchers, highlight some of the issues around curation and standardisation and discuss some of the methods and tools available to overcome some of these issues

Summary

Introduction

Due to the pressures in the pharmaceutical industry of increasing drug development costs, greater requirements for safer medicines and desire for prescribers to show value for money, over the last 5-10 years the industry has changed such that increasingly early drug discovery is being undertaken by SMEs (small to medium sized enterprises) and in academic groups. Almost all public databases are using the v2000 molfiles [9] as the preferred way of storing chemical structures and these have some limitations in their ability to represent certain types of compounds. Some types of 1,5 tautomers, such as the structures shown, would not be identified as the same compound from the Standard InChI.

Results

Conclusion