On-line Help for Ligand Expo

Name, Formula and SMILES Search

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:

Molecular formula search options:

Note: formulas must be entered with spaces, e.g.: C6 H11 N2 O7 P.

Molecular name search options:

SMILES search options:

InChi search options:

Instance Search

The input to an instance search is a 3-letter-code component identifier, and will result in a table of all PDB entries containing the desired component. The Display option will provide the information in two ways:

Each instance is individually available for download in PDB, MOL/SDF, and mmCIF formats. You can also launch the MarvinSketch viewer to look at the chemical structure in this instance.

Browse Search

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.

To measure similarity or distance in chemical space we precompute a chemical fingerprint for each chemical component in our dictionary. Our chemical fingerprint was developed by Christian Laggner for the OpenBabel software system. The fingerprint contains the SMILES patterns for approximately 1000 chemical features such as the presence of common functional groups or ring systems. Each component is tested for the presence the chemical patterns in the fingerprint. The results are stored in vector bits in which 1 or 0 is set to denote the presence or absence of a particular feature. Two fingerprints (A and B) are compared by using the Tanimoto similarity score, a value between 0 and 1, which is defined as:

Tanimoto score = (A .AND. B) / ( A + B - (A .AND. B) )

is the number of bits set in fingerprint A
is the number of bits set in fingerprint B
(A .AND. B)
is the number of bits set after calculating the bitwise logical AND between A and B
Note that the results of the SMILES and fingerprint comparison may produce some unanticipated results. The SMILES comparison will match substructures of the target molecule within any other component in our chemical dictionary. For small or simple targets (e.g. alanine), this may result is a large number of matches. Results of the chemical fingerprint comparison reflect the bias of the patterns in our chemical fingerprint. The discrimination of this comparison may be useful for locating molecules which have some common features but not with the selectivity of a substructure match.

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