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   Last Modified

   3 July 2017

Theoretical Organic Chemistry Nuclear Receptor Chemistry Structural Bioinformatics Rational Drug Design

3D Quantitative Structure-Activity Relationship

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Structure-Based and Ligand-Based 3D QSARs

Structure-based and Ligand-based 3D QSAR Protocols

 

The 3D QSAR method is categorized to the structure-based and ligand-based manners, respectively.

The structure-based 3D QSAR is only available for the case where the 3D structures of a target protein or its homologue bound to the active compound has been experimentally solved using the X-ray crystal structure analysis.

When a homology-modeled target protein is used for this purpose, the numerous combinations of the side chain rotamers in the ligand-binding site must be considered in order to obtain a linear relationship between the in vitro activity of the compounds and the interaction energy (or score) of the complexes.

On the other hand, the ligand-based 3D QSAR is useful, when a fine 3D structure of the target protein are not known experimentally.

 

Pharmacophore Mapping

Moreover, if a linear relationship is given from the ligand-based 3D QSAR, a receptor image obtained from the superposed structures is mapped by the pharmacophore characteristics of the active compounds, and this receptor image can be further used for the docking study.

 

 

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