Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot.
Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.
This form searches the chemical component dictionary by molecular name, molecular formula, or SMILES description. A number of search types are supported:
Chemical Component Identifier search options:
-Matching the chemical component identifier (3-letter-code)
-Matching chemically similar chemical components identified by a 3-letter-code using a fingerprint comparison.
Molecular formula search options:
-Exact all atom formula matches
-Exact heavy atom formula matches
-An exact formula subset query will match any exact partial dictionary component. For instance, a query for C6 N2 will match any formula containing exactly six carbons and two nitrogens.
-A formula subset query will find molecules whose formula contains a minimum of the query formula composition. For instance, C6 H7 Hg N2 O2 S will match C8 H10 Hg N2 O4 S.
-A close formula query will find molecules whose compositions differ by +/- three for any element in the query formula
This powerful search tool, which uses the MarvinSketch 2D drawing applet, serves three functions:
1. to upload/build a query molecule for a substructure search of the chemical component dictionary
2. to build a novel annotated chemical component definition
3. to convert chemical component descriptions between different formats for external use
The Browse feature allows the user to explore the content of the wwPDB chemical dictionary in a number of categories. Menus are provided to select amino acids, nucleotides, selected top-selling pharmaceuticals, and common aromatic ring systems. Searches are performed by finding structures containing a SMILES pattern or by comparison to a chemical fingerprint. The chemical fingerprint consists of 1000 individual chemical features such as the presence of common functional groups or ring systems. Fingerprints are considered similar if their Tanimoto similarity score is greater than 0.8. Within your query results are links to the chemical component listing, downloadable coordinates, and clickable links to search for further analogs by similar name, similar SMILES string, or similar chemical formula.
Sponsor: It is supported by funds from the National Science Foundation (NSF), the National Institute of General Medical Sciences (NIGMS), the Office of Science, Department of Energy (DOE), the National Library of Medicine (NLM), the National Cancer Institute (NCI), the National Center for Research Resources (NCRR), the National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institute of Neurological Disorders and Stroke (NINDS), and the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK).
|Synonym=Ligand Expo |Is part of=Rutgers University; New Jersey; USA |Has role=3D spatial image, Database |SuperCategory=Resource |DefiningCitation=http://ligand-depot.rutgers.edu/ |Id=nif-0000-21237 |CurationStatus=uncurated |Keywords=element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, ch
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