Molecular volume overlap

Thomas et al. were first to report a CoMFA QSAR pharmacophore model for anandamide (4) audits analogs (Thomas etal. 1996). These authors used molecular dynamics studies to explore conformations of 4 that present pharmacophoric similaritieswith2l -THC(l). A J-shaped or looped conformation of 4 was identified that had good molecular volume overlap with 1 when (1) the carboxyamide of 4 was overlaid with the pyran oxygen (0-5) in 1 (2) the head group hydroxyl of 4 was overlaid with the C-1 phenolic hydroxyl group of 1, (3) the five terminal carbons of the 4 fatty acid acyl chain were overlaid with the C-3 pentyl side chain of 1 and... 

Figure 8 Molecular volume overlap programs of Masek et al. as applied to a pair of angiotensin II antagonists. Note that not all the conformers considered in the over lap calculations are shown.

Walls and Sternberg210 considered surface complementary for docking protein-protein complexes using a vdW-like soft core potential. The use of accessible surface area on binding and complexation has been discussed, for example, by Flower.205 Surface descriptors have been used to calculate solvation energies as part of the energetics of molecular association.144,188,211 Volume overlap was also used to quantify interactions of chemical compounds.201 The HINT exponential function and empirical atomic... 

The definition of the cavity (shape and size) is an intricate and delicate question that may have a considerable influence on the results (even qualitatively). In the original Onsager s theory, the molecular cavity was defined as a sphere and the volume was taken equal to the partial molecular volume of the solute in the solution. In practice, this volume can be assumed to be equal to the average volume in the pure liquid. Experimental values are then easily deduced from the experimental density of the liquid at 20°C when this quantity is available. Obviously, in SCRF applications, it became rapidly necessary to achieve a theoretical definition of the cavity applicable to any molecular structure. In former works carried out by our group [28,62], it was shown that a simple linear relationship exists between the experimental volume derived from the liquid density (Onsager s recipe) and the van der Waals volume, i.e., the volume enclosed by a set of overlapping atomic spheres with Bondi radii [63], Roughly, this relationship is... 

Payne and Glen (105) studied several different aspects of molecular recognition with genetic algorithms. Conformations and orientations were determined which best-fit constraints such as inter- or intramolecular distances, electrostatic surface potentials, or volume overlaps with up to 30 degrees of Ifee-dom. 

Bondi developed a method based on covalent bond distances and van der Waals radii to calculate van der Waals volume [Bondi, 1964]. The volume calculated in this way is sometimes called the Bondi volume. It is obtained easily by summing appropriate volume contributions of atoms and functional groups, as proposed by Bondi note that the Bondi volume does not account for the overlaps which are possible whenever three or more atomic spheres intersect it is roughly 60 - 70 % of the -> molecular volume. 

The most common steric descriptors are - molar refractivity, -> surface areas and several - volume descriptors such as molecular volume. Other steric descriptors are -> steric interaction fields, MTD descriptors, -> common overlap steric volume, and several topological descriptors accounting for both size and - molecular branching. Other popular molecular steric descriptors are listed below. 

OpenEye company provides software to the pharmaceutical industry for molecular modelling and chemoinformatics. Their Shape TK module facilitates the calculation of molecular descriptors for shape volume overlap between molecules and spatial similarity of chemical groups [44],... 

These density functions form the underlying physical basis of two families of similarity computations, one which equates shape similarity with volume overlap and the other with surface congruence. In each case, molecular similarity can be... 

The ligand overlap techniques we have considered so far use distances between ligand centers to determine potential pharmacophores. An alternative technique is to use overlap or difference measures of more continuous molecular properties, such as molecular electrostatic potential and molecular volume,... 

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