AffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB
By P. Block, C. Sotriffer, Ingo Dramburg, Gerhard Klebe. 2005
87 citations recorded by the source corpus.
AffinDB is a database of affinity data for structurally resolved protein–ligand complexes from the Protein Data Bank (PDB). It is freely accessible at . 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.
Subfields: Materials Chemistry, Molecular Biology
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In Molecular Biology
Citations in the corpus
- ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “PDBBind (9), Binding MOAD (10) and AffinDB (11) contain binding affinity information for protein–ligand complexes found in the Protein Data Bank (PDB, 12).”
- BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities (2006, background): “Thus, BindingDB’s data collection differs significantly from those of databases which only collect affinities for protein–ligand complexes in the PDB, notably BindingMOAD (10) which holds 1400 data, PDBBind (11,12) with 1600 data, and AffinDB (13) with 750 data.”