Three dimension database searching

The Cambridge Crystallographic Data Center (http //www.ccdc.cam.ac.uknow provides a computerized database of more than 200,000 small molecular structures. In addition to this extensive structural database, the Cambridge group has developed a suite of programs for systematic structure search and retrieval. The most unique aspect of these programs is that database search queries can specify desired structures in three dimensions. 

Two factors contribute to the difficulty of searching 3D databases. First is the difficulty in specifying the search parameters. How are similar shapes defined Second, although the conformation stored in the database may be the most probable conformation (either the crystal structure or an energy minimum), in some cases a higher energy conformation is the biologically active one. Therefore, conformational flexibility should be included in the search process.Different methods have been developed to carry out searches in three dimensions. Detailed introductions to the problems and methods of 3D... 

Similarity is very subjective, as it depends on what are we looking for and from what point of view we are looking. For example, from a mathematical point of view, we would denote two molecules as similar if they have common features in three dimensions, whereas if we take a chemical approach, we would denote two molecules as similar if they had similar physical properties. Similarity-based methods have gained popularity due to the rapid technological progress and increased number of entries in chemical databases. This has made the application of computational search methods a necessity. 

In the following, we first present how contact graphs define the conformational search space of RNAs, to position and orient all nucleotides in three-dimensions. Then, a database of spatial relations based on molecular contacts, as observed among pairs of nucleotides in known structures, is introduced. 

FIGURE 16.3. Input and output from the Cambridge Structural Database. Morphine has been chosen as an example, (a) Search for the crystal structure of morphine. This can be done by name, atomic connectivity, or REFCODE (as in this example). The input was simply the first three lines shown above. The output follows (at REFC ) and includes the journal reference, space group, unit-cell dimensions, R factor, etc. (b) Output of atomic coordinates from the input at the top of (a). Courtesy the Cambridge Structural Database. 

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