Molecular field descriptors

Schuffenhauer A, Gillet VJ, Willett P. Similarity searching in files of 3D chemical structures analysis of the BIOSTER database using 2D fingerprints and molecular field descriptors. J Chem Inf Comput Sci 2000 40 295-307. 

One of the most attractive features of the CoMFA and CoMFA-like methods is that, because of the nature of molecular field descriptors, these approaches yield models that are relatively easy to interpret in chemical terms. Famous CoMFA contour plots, which are obtained as a result of any successful CoMFA study, tell chemists in rather plain terms how the change in the compounds size or charge distribution as a result of chemical modification correlate with the binding constant or activity. These observations may immediately suggest to a chemist possible ways to modify molecules to increase their potencies. However as demonstrated in the next section, these predictions should be taken with caution only after sufficient work has been done to prove the statistical significance and predictive ability of the models. 

The retrieval of all 3D structures from a database considered to be similar to a given target structure is comparable with 2D similarity searching. 3D similarity searching raises the problem of conformational flexibility. Schuffenhauer et analysed the BIOSTER database by similarity search using 2D fingerprints and molecular field descriptors. A comprehensive overview on pharmacophore perception and 3D database searches is given in references 101 and 102. 

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