3D Molecule Representation of Structures

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

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 ... 

To calculate 3D-MoRSE descriptors (3D-MOlecule Representation of Structures based on Electron diffraction, or simply MoRSE descriptors), Gasteiger et al. ]Schuur and Gasteiger, 1996,1997] returned to the initial I(s) curve and maintained the explicit form of the curve. As the atomic weighting scheme w, various physico-chemical properties such as atomic mass, partial atomic charges, and atomic polarizability were considered. To obtain uniform-length descriptors, the intensity distribution I(s) was made discrete, calculating its value at a sequence of evenly distributed values of, for example, 32 or 64 in the range of 1-31 A . Clearly, the more the values are chosen, the finer the resolution in the representation of the molecule. 

In the three-dimensional (3D) approach the 3D structure (see Structure Generators) of a molecule is transformed into a structure code. This is performed by regarding every atom pair in the molecule as a point scatterer and calculating the center symmetric diffraction pattern of the molecule as it would be obtained from an electron diffraction experiment. Based on these equations the 3D molecular representation of structures based on electron diffraction (3D-MoRSE) code has been developed. The 3D-MoRSE code is calculated using the equation... 

Many different structural descriptors have been developed for similarity searching in chemical databases [4] including 2D fragment based descriptors, 3D descriptors, and descriptors that are based on the physical properties of molecules. More recently, attention has focused on diversity studies and many of the descriptors applied in similarity searching are now being applied in diversity studies. Structural descriptors are basically numerical representations of structures that allow pairwise (dis)similarities between structures to be measured through the use of similarity coefficients. Many diversity metrics have been devised that are based on calculating structural (dis)similarities, some of these are described below. 

On a point of interest, the Cambridge Structural Database (8) archives crystal structure data (currently approx 153,000 small molecules) and enables searches to be performed using a graphical interface. Entries for terpenes, alkaloids, and miscellaneous natural products are identified as such, which is useful for searching these classes of compounds. The number of compounds in these three categories, with coordinates to enable 3D representation of structure, currently stands at approx 3700. 

Once the molecule is designed on a symbolic level, then the 3D structures of the conformational surface are directly constructed by using the 3D coordinate representations of the symbolic models, which are also coded in the template library. Cohen s procedure and related ones, however, are limited by the size and the nature of the sets of templates and assembly rules. The latter are not large enough to provide 3D building for complicated molecules such as bridged and polycyclic systems. For example, it is known that Cohen s script system often fails in generating 3D models of polycyclic molecules with more than three cycles. 

To code the configuration of a molecule various methods are described in Section 2.8. In particular, the use of wedge symbols clearly demonstrates the value added if stereodescriptors are included in the chemical structure information. The inclusion of stereochemical information gives a more realistic view of the actual spatial arrangement of the atoms of the molecule imder consideration, and can therefore be regarded as between the 2D (topological) and the 3D representation of a chemical structure. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

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