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AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB
- Block, Peter, Sotriffer, Christoph A., Dramburg, Ingo, Klebe, Gerhard
- Nucleic acids research 2006 v.34 pp. D522
- databases, drugs, ligands, molecular weight, nucleic acids, pH, temperature
- AffinDB is a database of affinity data for structurally resolved protein-ligand complexes from the Protein Data Bank (PDB). It is freely accessible at http://www.agklebe.de/affinity. Affinity data are collected from the scientific literature, both from primary sources describing the original experimental work of affinity determination and from secondary references which report affinity values determined by others. AffinDB currently contains over 730 affinity entries covering more than 450 different protein-ligand complexes. Besides the affinity value, PDB summary information and additional data are provided, including the experimental conditions of the affinity measurement (if available in the corresponding reference); 2D drawing, SMILES code and molecular weight of the ligand; links to other databases, and bibliographic information. AffinDB can be queried by PDB code or by any combination of affinity range, temperature and pH value of the measurement, ligand molecular weight, and publication data (author, journal and year). Search results can be saved as tabular reports in text files. The database is supposed to be a valuable resource for researchers interested in biomolecular recognition and the development of tools for correlating structural data with affinities, as needed, for example, in structure-based drug design.