Molecules representations

Caladadons 3D molecule representation X ACD/3D Chem3D X X SymApps - - X IMol - -... 

D Molecule Representation of Structures Based on Electron Diffraction Code (3D MoRSE Code)... 

Closely related to analytical interpretations of QSAR models is the ability to visualize the SAR trends encoded in a model. The glowing molecule representation developed by Segall et al. (14) is an example of direct visualization of a predictive model in terms of the actual chemical structure. Figure 1 shows such a representation, where the shading corresponds to the influence of that sub-structural feature on the predicted property. This type of visualization allows the user to directly understand how structural modifications at specific points will affect the property or activity being optimized. 

An interesting variant of whole-molecule representations is the use of internal coordi-... 

A set of thirty different descriptors [Stanton and Jurs, 1990] which combine shape and electronic information to characterize molecules and therefore encode features responsible for polar interactions between molecules. The molecule representation used for deriving CPSA descriptors views molecule atoms as hard spheres defined by the - van der Waals radius. The - solvent-accessible surface area SASA is used as the molecular surface area it is calculated using a sphere with a radius of 1.5 A to approximate the contact surface formed when a water molecule interacts with the considered molecule. Moreover, the contact surface where polar interactions can take place is characterized by a specific electronic distribution obtained by mapping atomic partial charges on the solvent-accessible surface. 

D-molecule representation of structures based on electron diffraction 3D-MoRSE descriptors... 

D-MoRSE 3D-Molecule Representation of Structures based on Electron diffraction descriptors... 

Many years later, it was found that this characteristic of the descriptor could be used for the correlation of biological activity and three-dimensional structure of molecules. The activity of a compound also depends on the distances between atoms (such as H-bond donors or acceptors) in the molecular structure [91]. Adaptation of the RBF function to biological activity led to the so-called 3D-MoRSE code (3D-Molecule Representation of Structures based on Electron diffraction) [92]. The method of RBF calculation can be simplified in order to derive a descriptor that includes significant information and that can be calculated rapidly ... 

Gasteiger et al. returned to the initial I s) curve and maintained the explicit form of the curve [36]. For A they substituted various physicochemical properties such as atomic mass, partial atomic charges, and atomic polarizability. To obtain uniform length descriptors, the intensity distribution I s) is made discrete, calculating its value at a sequence of evenly distributed values of, for example, 32 or 64 values in the range of 0 - 3lA. The resolution of the molecule representation increases with higher number of values. The resulting descriptor is the 3D MoRSE (Molecular Representation of Structures based on Electron diffraction) Code. 

D Molecular Descriptors are molecule representations based on Cartesian coordinates and Euclidean distances. 

Fig. 4. Projection of the point-molecule representation of the nine molecules using the Carbo index obtained from a gravitational-like similarity measure. The studied property is the boiling point...

Figures 1 to 4 show the projections of the point-molecule representation for the P-diketone compounds described in Table 1, on...

Figures 5 to 8 show projections of the Point-Molecule representation for Cu(II)-P-diketones quelate compounds, on the plane of two principal components for the Cioslowski-like, Coulomb-like, overlap-like and triple density similarity measure matrices, respectively. As before, the figures represent two-dimensional projections of 10-dimensional polyhedrons and the elements of the set are divided in two classes, depending on their respective extraction constant (K ). We can see that the most active compounds (represented by circles) can be shown split from the less active ones (represented by squares).

Figures 13 and 14 are projections of the Point-Molecule representation for retinoid compounds of Table 3, in the plane of two principal components of the similarity matrix. The elements of the set...

Figure 1.-Projection of the Point-Molecule representation, for beta-diketone compounds of Table 1, from a Cioslowski-like similarity measure.

Figure 7.-Prqjection of the Point-Molecule representation for Cu(U)-beta-diketones quelate compounds, from an overlap-like similarity measure.

---