Biological structure data sources

Biological, or fate, data provide the basis to the development of the quantitative structure-activity relationships (QSARs) described in this book. This introduction to data sources is not meant to be comprehensive, but to provide information on some of the more easily accessible and useful data sources, particularly in the environmental field. This includes the toxic effects of chemicals on aquatic and terrestrial organisms. 

Only recently, initiatives have been started to create freely available data sources such as PubChem,36 ChEBI,37 DrugBank,38 and HMDB,39 to mention some of them. These public databases collect publicly available information on compounds, their structures, their physical formulations (e.g., PubChem Substance), their targets, and their effects on biological processes. However, these databases are far from covering the entire spectrum of chemical information that can be linked to biology and pharmacology. 

Physicochemical properties that are based solely on the structure are stored in the data warehouse, but properties that are data-source dependent, such as citation or biological activity, are only referenced. A typical use of a chemical warehouse is to search for a set of... 

The Protein Data Bank (PDB) [5] is a computerized archive for the three-dimensional structural data on biological macromolecules - proteins and nucleic acids. Each protein structure reported has an identifying code (IDCODE), a header record containing useful information on the protein such as the name and source of the protein and the resolution of the structure, together with a series of references to published articles on the protein. Data are included on the refinement methods used, such as the programs used, the R value, the number of Bragg reflections, the root-mean-square deviations of the bond lengths and... 

Protein data bank showing 3D biological macromolecular structure data. Available at http //www.rcsb.org/pdb White JS and White DC (1997) Source book of enzymes. Boca Raton CRC Press. 

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