Probe interaction calculations

D structure conversion programs, 3-D database and search systems , probe interaction calculations, and distance geometry provides the necessary tools to make de novo discovery possible. Several recent reviews on these techniques are recommended. ... 

Developing a pharmacophore model using methods such as systematic conformational search, QSAR, distance geometry, and probe interaction calculations. 

CoMFA is based on interactions between a molecule and a probe traditionally, the probe has the properties consistent with a van der Waals sp3 carbon and a charge of +1.0. The interactions calculated between the probe and the molecules of interest are steric (van der Waals 6-12) and electrostatic (Coulombic with a 1/r dielectric) energies (4). The CoMFA process starts by constructing a 3D grid... 

Now, as experimental estimates of dipole moments of molecules in solution are scarce, we must probe the calculated converged charge density by analyzing results for other properties. One possibility is to analyze the solute-solvent interaction, and that can be obtained by solvent shifts in UV-vis or NMR spectra for example. 

The effect of an electrical field on the absorption/emission of spectra of a probe such as fluorescein or a coumarin derivative. It is derived from the interaction of the induced dipole(s) in the probe interacting with the charged group. See Sitkoff, D., Lockhart, D.J., Sharp, K.A., and Honig, B., Calculation of electrostatic effects at the amino terminal of an helix, Biophys. J. 67,2251-2260,1994 Pierce, D.W. and Boxer, S.A., Stark effect spectroscopy of tryptophan, B/opfiyx. J. 68,1583-1591,1995 Klymchenko, A.S., Avilov, S.V., and Demchenko, A.P., Resolution of Cys and Lys labeling of a-crystalUn with site-sensitive fluorescent 3-hydroxyflavone dye. Anal. Biochem. 329, 43-57, 2004. 

When a probe binds a target molecule, it may displace ordered water molecules and it may result in ordering of a flexible part of the protein. Both these events have entropic effects. To account for these, an entropy term has been included in more recent versions of GRID and takes different forms according to the type of calculation. It is computed when parts of the target are treated as flexible, when the probe interactions are compared to that of water, and for the hydrophobic probe, known as the DRY probe. 

The selected 3D interaction points are used to calculate enzyme fingerprints using the GRIND technology [18]. For each CYP-probe interaction map (see Fig. 

Inverse gas chromatography at infinite dilution appears to be a powerful tool for studying the surface properties of carbon fibres and polymer matrices. The use of alkane probes and acid/base probes allows the characterization of the surfaces in terms of their London dispersive component of surface energy and their acid/base or acceptor/donor characteristics. A strong correlation was obtained between fibre-matrix adhesion, measured by a destructive fragmentation technique, and the level of acid base interactions calculated from the chromatographic analysis. 

Comparative Molecular Field Analysis The basic idea of Comparative Molecular Field Analysis developed by R.D. Cramer et al. (Tripos CoMFA ) is that a suitable sampling of the steric and electrostatic field around a ligand molecule may provide all the information necessary for explaining its biological property in a 3D-QSAR. The steric and electrostatic contributions to the total interaction energy between the ligand and a chosen probe are calculated... 

Since this article is concerned with protonation reactions, some mention of earlier related work on the more classical alkylidyne-metal complexes is appropriate. The proton has proved a popular experimental probe for examining the reactivity of alkylidyne-metal complexes in studies attempting to establish the nature of the M=C bonding interaction. Calculations by Kosti6 and Fenske (20) on Fischer-type alkylidynes suggest that the metal-carbon bond is generally polarized —C ", but that the... 

Coulomb potential functions and the standard Tripos CoMFA probes (the Csp probe was used for calculation of steric interactions and the probe for calculation of elec-bostatic interactions, respectively). A PCA (factor analysis without axes rotation) was done on the descriptor matrix and a classification of the heteroaromatic substiments into families was performed using the Sybyl hierarchical clustering procedure of the obtained principal component... 

Furthermore the interaction calculations were applied to estimating the electric field strength in the zeolite supercage. In Table 2 the values calculated applying equation 6 [79,85] are opposed to those obtained experimentally with nitrogen [89], which have been converted taking deviations from a parallel alignment of the probe molecule 6 = 0) into account. The calculated data are shown to be reproduced within the limits of experimental inaccuracy. 

Being endowed with more degrees of vibrational freedom the use of triatomic probes should in principle enlarge the information on interaction. Extending the interaction calculations to linear triatomics like CO2 and N2O in partly alkaline earth ion-exchanged zeolites A stable sorption sites were found between adjacent SI cations due to the enlarged dimension of these molecules. 

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