Three-dimensional Structure Generation Automation

Stereochemistry Representation and Manipulation Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Generation Automation Three-dimensional Structure Searching Topological Indices Topological Methods in Chemical Structure and Bonding. 

Cambridge Structural Database De Novo Ligand Design Pharmacophore and Drug Discovery Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structure Databases Three-dimensional Structure Generation Automation Three-dimensional Structure Searching. 

Green DVS. Automated three-dimensional structure generation. In Martin YC and Willett P, editors, Designing bioactive molecules. Three-dimensional techniques and applications. Washington DC, American Chemical Society, 1998 47-71. 

The three dimensional structure was obtained by means of single crystal X-ray diffraction. CuKa radiation, a graphite monochromator, and a photomultiplier tube were used to collect 1825 total reflections on an automated diffractometer. Of these, 1162 were used for the analysis. Figure 2 shows a computer generated drawing of halcinonide. The position of the chlorine atom was not clear from the Patterson map, but the direct method program "MULTAN" gave its position. 

Finally, the electron microscope will become the dominant instrument for studying protein machines in vitro and in situ. Tomographic methods applied to single cells and molecules combined with automated reconstruction methods will generate models of protein-based structures that cannot be determined by x-ray crystallography. High resolution three-dimensional models of molecules in cells will help explain the intricate biochemical interactions among proteins. 

The type of features that are typically used in our size and shape searching are generic 3D triangle and 3D tetrangle features which are derived from 3D structures generated by the CONCORD program (see Three-dimensional Structure Generation Automation). 

Gasteiger and co-authors recently suggested a new approach. They developed a molecular transform, derived from an equation used in electron diffraction studies, that allows the presentation of the 3D structure of a molecule by a fixed (constant) number of variables. On the other hand, a generator of 3D structures of organic compounds was created (see Three-dimensional Structure Generation Automation). This made it possible to study the correlations between 3D structures and infrared spectra using ANN. 

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