Ligand Depot (ligand-depot.rutgers.edu) is a data warehouse that integrates databases, services, and tools related to small molecules bound to macromolecules. The initial release (v. 1.0, November, 2003) focuses on providing chemical and structural information for ligands that are found as part of the structures deposited with the PDB.
Ligand Depot allows users to extract ligand information from the PDB, to perform chemical substructure searches, and to search other small molecule resources on the Web. One of the distinguishing features of Ligand Depot is that it allows users to retrieve the coordinates of any small molecule found within the structure entries of the PDB. It is also updated daily and therefore provides the most current information on small molecules present in the PDB.
Ligand Depot currently includes chemical descriptions for the ~4,600 ligands that are part of the structures deposited in the PDB, and it offers various search options for obtaining information on these small molecules. It accepts keyword queries based on PDB ligand code, compound name and chemical formula. Using a simple graphical interface, a substructure search may also be performed between a small molecule of interest and all of the ligands present in the PDB.
Ligand Depot can also be used to browse a variety of other small molecule resources on the Web. Information from 70 small molecule sites are stored in Ligand Depot. These resources are organized into four categories, including molecular visualization sites, commercial sites, nomenclature sites, and chemical databases. Keyword searches may be performed on these external Web sites if they are search-enabled. Thus, information on ligands can be extracted from a diverse collection of Web resources using a single query.
A helpful tutorial for using Ligand Depot is accessible atligand-depot.rutgers.edu/html1/User_Guides.html.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
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National Institutes of Health, and the
US Department of Energy.