Advantages and disadvantages

The main advantages of the 3D-QSAR method are:

• The structure of the target site is not required.

• It does not require the input of either experimentally determined or calculated parameter values.

• It gives a visual picture that is easier to interpret than the mathematical formula of traditional QSAR.

• It is not restricted to a study of molecules with similar structures; it only requires similar pharmacophores.

• It allows the activities of new molecules to be predicted without synthesising them.

• The same general method of generating the 3D-QSAR model is followed for all studies. The main disadvantages are:

• It is limited to predictions in the three-dimensional space covered by the training set.

• A model cannot give reliable predictions for substituent structures that do not lie in the structural confines of the original model. For example, if the model was obtained using a training set where only methyl substituents were present in a certain position it is not possible to get a reliable prediction for compounds in which that methyl is replaced by, say, a propyl group.

• It may be difficult to correctly align members of the training group, especially if it contains members with diverse structures.

• The members of the training set must interact with the target in similar ways.

• The accuracy of the analysis is dependent on the grid spacing employed.

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