Molecular similarity measures

In the original kNN method, an unknown object (molecule) is classified according to the majority of the class memberships of its K nearest neighbors in the training set (Fig. 13.4). The nearness is measured by an appropriate distance metric (a molecular similarity measure as applied to the classification of molecular structures). It is implemented simply as follows ... 

Rarey M, Dixon JS. Feature trees a new molecular similarity measure based on tree matching. / Comput Aided Mol Des 1998 12 471-90. 

Pan, D., Iyer, M., Liu, J., Li, Y., Hopfinger, A. J., Constructing optimum blood brain barrier QSAR models using a combination of 4D-molecular similarity measures and cluster analysis descriptors. J. Chem. Inf. Model. 2004, 44, 2083-2098. 

Mezey, P.G. (1996) Molecular similarity measures of conformational changes and electron density deformations. In Advances in Molecular Similarity, Vol. 1, p. 89. 

Mezey, P.G. (1995) Density domain bonding topology and molecular similarity measures., In Topics in Current Chemistry, Vol. 173, Molecular Similarity, Sen, K. (Ed.), Springer-Verlag, Heidelberg. 

Mezey, P.G. Density Domain Bonding Topology and Molecular Similarity Measures. 173, 63-83 (1995). 

Sola, M., J. Mestres, R. Carbo, and M. Duran. 1996. A Comparative Analysis by Means of Quantum Molecular Similarity Measures of Density Distributions Derived from Conventional ab initio and Density Functional Methods. J. Chem. Phys. 104, 636. 

Currently, the most exciting work on the shape function is being done in the fields of atomic and molecular similarity. One certainly expects the shape function to continually appear as those fields continue to progress. However, the role of the shape function in those fields is presently incidental the shape function appears, but underlying theory plays no essential role. It would be interesting to develop molecular similarity measures that exploit the insights from the shape-functional pictures of electronic changes. 

Maggioea, G.M. and Shanmugasundaeam, V. Molecular similarity measures. In Chemometrics Methods and Protocols, Bajoeath, J. (Ed.). Humana Press, Totowa, NJ, 2003, 1-50. Willett, P., Barnard, J.P., and Downs, G.M. Chemical similarity searching. 

Ginn CMR, Willett P, Bradshaw J. (2000) Combination of Molecular Similarity Measures Using Data Fusion. Perspect. Drug Discov. Des. 20 1-16. 

Subheading 2.5. provides a very brief discussion of molecular dissimilarity measures that are basically the complement of their corresponding molecular similarity measures. This section also presents reasons as to why similarity is preferred over dissimilarity, except in studies of diversity, as a measure of molecular resemblance. 

Ginn, C. M. R., Willett, R, and Bradshaw, J. (2000) Combination of molecular similarity measures using data fusion. Perspec. Drug Disc. Design 20, 1-16. 

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