Molecular superpositions

Redington, P.K. MOLFIT a computer program for molecular superposition. Comput. Chem. 1992, 36, 217-222. 

Silverman, B. D. and Platt, D. E. (1996) Comparative molecular moment analysis (CoMMA) 3D-QSAR without molecular superposition. J. Med. Chem. 39, 2129-2140. 

Miller, M. D., Sheridan, 1C P., Kearsley, S. K. (1999) SQ a program for rapidly producing pharmacophorically relevant molecular superpositions. J Med Chem 42,... 

Keywords K-Opioid receptor Agonist Molecular superposition Pharmacophore ... 

Pharmacophore Extraction Through a Series of Molecular Superpositions..293... 

Fig. 15 K-Agonists in training set and their property spheres. Training set comprising four morphinans (TRK-820, KNT-63, KNT-62, and NS-22), two arylacetamides (U-69593 and U-50488H), and one neoclerodane diterpene (salvinorin A). The spheres on each molecule are property spheres for molecular superposition. The colors of the spheres indicate the following properties hydrophobic (HP, black)-, aromatic (AR, green)-, hydrogen-bond donors (HD, blue)-, hydrogen-bond acceptors (HA, red)-, and hydrogen-bond donors/acceptor (DA, violet). Large and small spheres indicate radii of 1 and 0.5 A, respectively. p/K = S, (p)/S i(K)...

Girones X, Robert D, Carbo-Dorca R. TGSA a molecular superposition program based on topo-geometrical considerations. J Comput Chem 2000 22 255-263. 

P. K. Redington, Comput. Chem., 16, 217 (1992). MOLFIT A Computer Program for Molecular Superposition. 

In this chapter only QSAR methods which use physicochemical or structural features of molecules will be discussed, while in Chapter 25 3D-QSAR approaches will be presented. These so-called 3D-QSAR techniques, e.g. CoMFA, use the basic statistical principles, such as partial least squares (PLS), of QSAR methods, but in addition use the three-dimensional characteristics of a molecule specifically related to electronic, steric and lipophilic field effects. In these methods the molecular superposition believed relevant to binding to the target is crucial. 

May and Johnson have taken the molecular superposition problem to the next level of complexity and used it to superpose proteins in order to measure structural similarity. Once molecules are as large as proteins, and pairs of proteins that may or may not be similar are tested, it is sometimes problematic to decide which pairs of atoms in the two structures should be used for the... 

Boon et al. also studied several chiral molecules, which included again two amino acids (Ala and Leu) and CHFClBr, a prototype of chiral molecules. Ab initio total molecular electron densities yielded both Euclidean distances and Carbo indices between the enantiomers of these molecules. Molecular superposition was performed with, on the one hand, a manual alignment based on chemical intuition and the QSSA method, on the other hand. When analyzing the tables of the work by Boon et al. and comparing the results to the work by Mezey et al., similar values for the Euclidean distances between the two enantiomers appear for Ala and Leu, which once again illustrates the power of the ASA promolecular densities to yield quantum similarity measures in good agreement with those obtained from ab initio calculations. 

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