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Visualization of the Chemical Space in Drug Discovery

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Chemical space has become a key concept in drug discovery. The continued growth in the number of molecules available raises the question regarding how many compounds may exist and which ones have the potential to become drugs. Analysis and visualization of the chemical space covered by public, commercial, in-house and virtual compound collections have found multiple applications in diversity analysis, in silico property profiling, data mining, virtual screening, library design, prioritization in screening campaigns, and acquisition of compound collections, among others. This review covers several techniques, computational programs and approaches that have been developed to visualize, navigate and study the chemical space of molecular databases. Techniques developed in our group are presented including a quantitative assessment of the multi-fusion similarity maps. Additionally an application of 3D-similarity, based on the overlay of chemical structures, to represent the chemical space is introduced. Several comparisons of the chemical space covered by compound collections from different sources such as combinatorial libraries, drugs and natural products, or directed to specific therapeutic areas are also discussed.

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Keywords: Chemoinformatics; combinatorial libraries; data mining; data-driven analysis; molecular diversity; multi-fusion similarity maps; structure-activity relationships; virtual screening

Document Type: Research Article

Publication date: December 1, 2008

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  • Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design. Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
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