Ligand superposition

Lemmen, C., Lengauer, T., and Klebe, G. ELEXS a method for fast flexible ligand superposition./. Med. Chem. 1998, 41, 4502-4520. 

Lemmen C, Lengauer T, Klebe G (1998) FlexS A method for flexible ligand superposition. J Med Chem 41 4502-4520... 

The Monte Carlo version of minimal steric difference (denoted as MCD) improves the computation of non-overlapping volumes in the standard-ligand superposition, translating thus the topological MSD parameter into the (3D) metric context (Mojoc et al. 1975 Ciubotariu et al. 1983). In order to calculate the MCD, the molecules are described by the Cartesian coordinates and vdW radii of their atoms. The atomic coordinates implicitly specify the way one achieves the superposition all molecules of the series are represented in the same Cartesian coordinate system. The mathematical method used in the MCD-technique for computation of nonoverlapping volumes is the Monte Carlo method (Demidovich and Maron 1987). 

There are two important points to emphasize with regard to Flf- First, contributions to Flf are not computed from first principles. Instead, the potential is constructed parametrically and the parameter values are determined by fitting calculated properties to experiment. Secondly, there are two distinct ways in which Flf can be constructed-globally or via ligand superposition. 

Totrov M (2008) Atomic property fields generalized 3D phar-macophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR. Chem Biol Dmg Des 71 15-27... 

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