Simple Fingerprints Structural Keys

Structural key is basically a string of values that describes the chemical composition and/or structural motifs that are present in the chosen substructure and each molecule in the database [66]. A structural key is usually represented as a boolean array, an array in which each element is TRUE or FALSE. A given bit is set to 1 (True), if a particular structural feature is present and a given bit is set to 0 (False), if it is not as shown in the following figure. A structural key is a bitmap in which each bit represents the presence (TRUE) or absence (FALSE) of a specific structural feature (pattern). The 1-th bit of this array, for example, can be used to represent any structural featme of the molecule. This list can include  

One important point to emphasize in the use of a structural key is that the definition of a particular array element must be chosen initially. This has the disadvantage that this key can become extremely long and is inflexible. Conversely, it is possible to optimize this structural key for the class of compounds present in the database (Fig. 1.33). 

1 Open-Source Tools, Techniques, and Data in Chemoinformatics 

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Databases can be searched by simple Boolean operations using both structural keys and fingerprints. The latter have a higher information density than structural keys without losing specificity. Hence, database searches using fingerprints instead of structural keys are more efficient. 

Similarity Search. A type of "fuzzy" structure searching in which molecules are compared with respect to the degree of overlap they share in terms of topological and/or physicochemical properties. Topological descriptors usually consist of substructure keys or fingerprints, in which case a similarity coefficient like the Tanimoto coefficient is computed. In the case of calculated properties, a simple correlation coefficient may be used. The similarity coefficient used in a similarity search can also be used in various types of cluster analysis to group similar structures. 

The key to this work is DNA—the chemical fingerprint present in every tissue of every individual. Although the general structure of DNA is the same from one person to another, evidence for familial ties is present in the detailed sequence of each person s DNA. With the use of relatively simple chemistry—involving fluorescent dyes or radioactive isotopes, enzymes, gel electrophoresis, and a process called the polymerase chain reaction (PCR) that earned its inventor the 1993 Nobel Prize in Chemistry (Section 25.8)—it is now easy to synthesize millions of copies from a sample of DNA and to sequence it rapidly and conveniently. Application of these tools to comparison of DNA samples from victims and relatives provides hope that, at least in some cases, the gap between family members will be closed. 

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