Protein–ligand interaction databases: advanced tools to mine activity data and interactions on a structural level

The formation of molecular complexes between proteins and small organic substances is a fundamental concept of life. Biochemical experiments from X-ray crystallography to isothermal titration calorimetry (ITC) are applied in large-scale providing data for the analysis of the structural foundations of binding affinity. In recent years, several, mostly publically available databases emerged containing affinity data and structural information. These databases are central for the construction of complex models describing interaction geometries and correlate structural features to the strength of binding. Binding affinity databases reflect the knowledge of affinity measurements from many sources, mostly scientific and patent literature. A critical aspect is the data quality, which is affected by transcription errors during database construction as well as experimental uncertainties. The Protein Data Bank (PDB) is the central resource for macromolecular biological structures containing nearly 100,000 data entries today. Sophisticated geometric databases have been constructed based on this allowing for complex queries about the spatial arrangement of functional groups and their interactions. For scientists working in molecular design like medicinal chemists, access to this information can substantially support the process of creating new molecular entities specifically interacting with proteins of interest. WIREs Comput Mol Sci 2014, 4:562–575. doi: 10.1002/wcms.1192 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.