Database topological

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

The 16 possible motifs shown in Figure 2.21b never occur. Even if this database is limited compared with the universe of existing proteins, the survey clearly demonstrates that a few topological arrangements occur much more frequently than others, and that most possible complex motifs never occur or occur only in a few cases. In 1995 a preliminary survey of a much larger database of known structures yielded the same basic conclusions. 

Hall, L. H., Kier, L. B. Molecular connectivity chi indices for database analysis and structure-property modeling. In Topological Indices and Related Descriptors in QSAR and QSPR, Devillers,... 

Ertl and co-workers [20] have developed such a method for generating a topological PSA (TPSA) based on 3D PSA values for 43 fragments resulting from an analysis of 34,810 compounds taken from the WDI database. The correlation between PSA and TPSA is very high (r2 = 0.982). 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

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