Encoding shape

Das S, Kokardekar A, Breneman CM (2009) Rapid comparison of protein binding site surfaces with property encoded shape distributions. J Chem Inf Model 49 2863-2872... 

Shape. Pharmacophores capture the key features of intermolecular interactions. However, they do not explicitly capture the shape and volume of the ligand, even if this is crudely implied by the largest four-point pharmacophore exhibited, and the totality of potential pharmacophores exhibited across a range of conformations encodes shape fragments. Hahn (47) has described a method for three-dimensional shape-based searching implemented in the Catalyst program. Seven... 

In the second class of phenomena are intermolecular interactions, where a certain degree of complementarity must be achieved for a reaction to occur. There must be a fit or recognition between molecules or between molecule and receptor, governed by the shape of each. The degree of fit or complementarity (similarity) has led to indexes encoding shape. 

Graph-based structure analyses had not been used for the specific objective of encoding relative shape. There was the frequent inference that indexes derived from these methods encode shape information, although none had been conceived with this specific objective in mind. It is from the graph of a molecule that we have derived the kappa indexes with the objective of encoding relative shape. 

Das, S., Krein, M. P., and Breneman, C. M. 2010. Binding affinity prediction with property-encoded shape distribution signatures.. Chem. Inf. Model. 

The superstructure of smooth muscle actin filaments is differentiated from those of striated muscle by the absence of the troponins and the lateral organization by association of the filaments with dense bodies instead of with the Z-line. How these differences are encoded is again not at all clear. However, the myofibrillar structure and the alignment of the alternating actin and myosin filaments is apparently due primarily to dense bodies and the actin-actinin macrostructures. As the bent dumbbell shaped actins assemble into filaments they are all oriented in the same direction. The S-1 fragments of myosin will bind to actin filaments in vitro and in... 

Each nervous impulse is a group of consecutive action potential bursts. It had been pointed out above that these bursts are identical in shape. The information to be transmitted by the impulse is encoded in terms of the number of individual bursts in a group and of the intervals between bursts. 

Fig. 1.11 Typical basic three-dimensional negative intensity directly before the actual imaging sequence with slice selection, frequen- read gradient. The shape of the 180° rf pulse cy encoding and phase encoding in three ortho- is drawn schematically to indicate that a soft gonal directions. The compensating lobe for pulse is used, the read gradient is drawn as a rectangle with...

Fig. 4.2.3 PGSE timing diagram where Gz denotes both the slice select and the pulsed, sinusoidal shaped displacement encoding gradient and Greacj displays the transverse imaging gradient.

The molecular descriptors refer to the molecular size and shape, to the size and shape of hydrophilic and hydrophobic regions, and to the balance between them. Hydrogen bonding, amphiphilic moments, critical packing parameters are other useful descriptors. The VolSurf descriptors have been presented and explained in detail elsewhere [8]. The VolSurf descriptors encode physico-chemical properties and, therefore, allow both for a design in the physico-chemical property space in order to rationally modulate pharmacokinetic properties, and for establishing quantitative structure-property relationships (QSPR). 

One should note that the phase shift becomes time-independent and maximal for a = 1, i.e., at the resonance condition v = vG. The frequency spectrum 4>(a) bears a sine shape with a bandwidth inversely proportional to the number of oscillations of the gradient field (Fig. 4). Such a behaviour was also predicted in Ref. 15. Recording in a systematic way the phase shift as a function of vG without space encoding would be a very fast and efficient method to scan in a whole object the possible frequencies of spin motions. 

This equation shows that the most relevant computational information on the drug-receptor complex is encoded both in reactivity (hydrogen bond donor propensity) and in shape descriptors. 

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