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The PDBSite database provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein–protein, protein–DNA and protein–RNA interactions) in the Protein Data Bank (PDB). The PDBSite is available online at http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/. It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure. The PDBSite is updated after each new PDB release.

The local DNA conformation in the region of transcription factor binding sites, determined by context, is one of the factors underlying the specificity of DNA-protein interactions. Analysis of the local conformation of a set of functional DNA sequences may allow for determination of the conservative conformational and physicochemical parameters reflecting molecular mechanisms of interaction. The web resource SITECON is designed to detect conservative conformational and physicochemical properties in transcription factor binding sites, contains a knowledge base of conservative properties for >100 high-quality sample sites and allows for recognition of potential transcription factor binding sites based on conservative properties from both the knowledge base and the results of analysis of a sample proposed by a user. The resource SITECON is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/.