Sammon map

Figure 15.5 Sammon map with SVM classification of drugs based on their volume of distribution (a) and plasma half-life (b) [95].

Ekins, S., Balakin, K.V., Savchuk, N. and Ivanenkov, Y. (2006) Insights for human efher-a-go-go-related gene potassium channel inhibition using recursive partitioning and Kohonen and Sammon mapping techniques. Journal of Medicinal Chemistry, 49,... 

Frickenhaus, S., Kannan, S., Zacharias, M. Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and sammon mapping. J. Comput. Chem. 2009, 30, 479-92. 

An overall picture of similarity between [C4CiIm][PFg] and conventional solvents is given by the so-called nonlinear map, or Sammon map [20] in Figure 9.5. The closer the points representing solvents on the map, the more similar the solvents are. As is seen, the position of the IL on the map is between esters and aromatic hydrocarbons. 

Figure 9.5 Sammon map representing similarity of extraction ability of solvents (with respect to extraction of neutral organic compounds). The closer the points are on the map, the more similar are the corresponding solvents. Conventional solvents are designated by numbers, some representative numbers are m-xylene—35, butyl acetate—9, 1-octanol—40. The point marked BMImPF, represents l-butyl-3-methyl-imidazolium hexafluorophosphate ([C4CiIm][PF5]).

PCA is not the only projection method that can be used. Various types of nonlinear projections have been employed, e.g., Sammon mapping and nonlinear PCA [80], and several software packages can be used to graphically visualize library distributions and aid compound selection [81]. 

Sammon maps and Kohonen maps have been used with a consistent training set (93 molecules) and test set (35 molecules) to compare the classification... 

Figure 8 Sammon map obtained for the training data set, showing the relative distances between the input variabies [ASE, A, NICS(1)zz, and HOMA] in the original space. The color scale indicates the Euclidean distances between the weight vector of each neuron and the neuron activated by benzene. ASE, aromatic stabilization energy HOMA, harmonic oscillator model of aromaticity NICS, nucleus-independent chemical shift A, magnetic susceptibility exaltation. Reprinted with permission from Aionso and Herradon (2010JCC917). Copyright 2009 Wiiey Periodicais, inc.

Figure 6. Sammon map of the xanthene, cubane, and adamantane libraries used by Gasteiger et al.

Agrafiotis, D. K., A new method for analyzing protein sequence relationships based on Sammon maps. Protein Sci., 6 (1997) 287-293. 

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