Conformational analysis shape representations

Figure 2 Structural alignment methods with continuous properties. Methods are based on continuous properties using the algorithms implemented in MSA (I), HASL (II), and CoMFA (III). A conformational analysis (optional) can be used to select candidate conformations ( bioactive conformation, or alternatively a set of biologically relevant conformations that are used for the alignment). The structure representation is based on molecular shape (I), a four-dimensional lattice (II). or molecular fields (III). The different algorithms for the alignment require that a reference be cho.sen so that comparisons between each ligand and the reference can be made. A statistical measure of molecular similarity is performed to identify the alignment that maximizes the molecular similarity between the ligands in term.s of three-dimensional overlap (MSA, HASL) or electrostatic potential distributions...

Preparatory to the shape analysis, the coordinate system is rotated by a similarity transform so that the 3x3 representation of S for each individual conformation is rendered in diagonal form. 

A molecule contains a nuclear distribution and an electronic distribution there is nothing else in a molecule. The nuclear arrangement is fully reflected in the electronic density distribution, consequently, the electronic density and its changes are sufficient to derive all information on all molecular properties. Molecular bodies are the fuzzy bodies of electronic charge density distributions consequently, the shape and shape changes of these fuzzy bodies potentially describe all molecular properties. Modern computational methods of quantum chemistry provide practical means to describe molecular electron distributions, and sufficiently accurate quantum chemical representations of the fuzzy molecular bodies are of importance for many reasons. A detailed analysis and understanding of "static" molecular properties such as "equilibrium" structure, and the more important dynamic properties such as vibrations, conformational changes and chemical reactions are hardly possible without a description of the molecule itself that implies a description of molecular bodies. 

In order to make the representation of structures in the computer prone to an efficient handling and searching, a variety of problems have to be solved unique and unambiguous representation, analysis of rings or shape, definition of structural similarity or diversity, handling of 3D structures, and conformational flexibility. 

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