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Predicting Molecular Interactions in silico: I. A Guide to Pharmacophore Identification and its Applications to Drug Design

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A major goal in contemporary drug design is to develop new ligands with high affinity of binding toward a given protein receptor. Pharmacophore, which is the three-dimensional arrangement of essential features that enable a molecule to exert a particular biological effect, is a very useful model for achieving this goal. If the three-dimensional structure of the receptor is known, pharmacophore is a complementary tool to standard techniques, such as docking. However, frequently the structure of the receptor protein is unknown and only a set of ligands together with their measured binding affinities towards the receptor is available. In such a case, a pharmacophore-based strategy is one of the few applicable tools.

Here we present a broad, yet concise guide to pharmacophore identification and review a sample of applications for drug design. In particular, we present the framework of the algorithms, classify their modules and point out their advantages and challenges.
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Keywords: computer-aided drug design; de-novo design; docking; lead generation; pharmacophore fingerprints; pharmacophore mapping; pharmacophore modeling; pharmacophore searching; receptor-based pharmacophore; virtual screening

Document Type: Review Article

Affiliations: School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

Publication date: 2004-01-01

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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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