Nonoverlap steric volume

The nonoverlap steric volume V on is another MSA descriptor defined as [Tokarski... 

Equations that have only linear terms in MSA descriptors suggest that there are no compounds more potent than the reference, because by definition there can be no compound that has a V value, or forecast potency, higher than that of the reference." To minimize the nonoverlap steric volume NV, the best we can do is to use the reference shape for which NVq will be zero and forecast potency equal to that of the reference. These problems result from lumping multiple regions of 3D space into one shape descriptor. Even when the most potent compound in the training set is close to the ideal, other 3D-QSAR methodologies might reveal bad steric contacts that could be removed to produce an increase in potency. 

Motoc, I., Holban, S., Vancea, R. and Simon, Z. (1977). Minimal Steric Difference Calculated as Nonoverlapping Volumes. Correlations with Enzymatic Hydrolyses of Ribonucleosides. Stadia Biophys., 66,75-78. 

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). 

The Monte Carlo version of minimal steric difference,designed hereafter as MCD, improves the computation of nonoverlapping volumes in the standard-molecule superposition by giving up the topological... 

The minimal steric difference concept allows a detailed description of steric structure - at about 1A precision, and is thus suited for description of steric fit. This precision may be nevertheless insufficient in certain instances, especially if imperfections of the superposition process are concerned. The Monte Carlo version (MCD) allows a practically unlimited precision in determining nonoverlapping volumes. The part of the receptor which interacts within the studied series of molecules can be mapped by the MTD-procedure, but this requires a large number of predictor variables (the 6j s). 

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