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Self-Organizing Maps in Drug Discovery: Compound Library Design, Scaffold-Hopping, Repurposing

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High-throughput screening campaigns are fuelled not only by corporate or “maximally diverse” compound collections, but increasingly accompanied by target- or bioactivity-focused selections of screening compounds. Computerassisted library design methods aid in the compilation of focused molecule libraries. A prerequisite for application of any such computational approach is the definition of a reference set and a molecular similarity metric, based on which compound clustering and iterative virtual screening are performed. In this context the self-organizing map (SOM, Kohonen network) and variations thereof have found widespread application. SOMs cover such diverse fields of drug discovery as screening library design, scaffold-hopping, and repurposing. Here we present the concept of the SOM technique along with recent case studies. Advantages, limitations and potential future applications are critically discussed.
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Keywords: Bioisosteric replacement; Kohonen network; chemical space; cheminformatics; database; drug design; leadhopping; molecular similarity; virtual screening

Document Type: Research Article

Affiliations: Chair for Chem- and Bioinformatics, Institute of Organic Chemistry & Chemical Biology, CMP / LiFF / ZAFES, Johann Wolfgang Goethe-University, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany.

Publication date: 01 January 2009

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  • Current Medicinal Chemistry covers all the latest and outstanding developments in medicinal chemistry and rational drug design. Each issue contains a series of timely in-depth reviews written by leaders in the field covering a range of the current topics in medicinal chemistry. Current Medicinal Chemistry is an essential journal for every medicinal chemist who wishes to be kept informed and up-to-date with the latest and most important developments.
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