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Curr Med Chem. 2004 Jan;11(1):71-90.

Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design.

Author information

1
School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel. oranit@tau.ac.il

Abstract

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.

PMID:
14754427
DOI:
10.2174/0929867043456287
[Indexed for MEDLINE]

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