Ligandbook provides text search of the metadata and a chemical sub-structure search.

The menu entry Search opens a new page with a graphical sketcher application.

1. Draw a characteristic sub-structure of your query molecule. Select tools from the menu to the left then click on the canvas to the right in order to apply the tool. Click on bonds or atom names to place them on the canvas. Click on existing elements to change them. The Del tool deletes atoms or bonds. New erases the canvas.
2. Submit the query with the Search button

The search will return all structures that contain the query structure.

Tips

• Make the query structure as specific as possible in order to reduce the number of results. Simple/small query structures are contained in many compounds and will therefore return large result lists.
• Instead of drawing one can also copy & paste a SMILES string into the input/output text field at the top of the Sketcher window. The sketcher will draw the SMILES so that you can modify it. Then conduct the search as described above.
• It is also possible to enter a compound name or the name of a drug in quotation marks in the Sketcher text field. For example, "ibuprofen" draws 2-(4-Isobutylphenyl)propanoic acid.

The search box in the upper left corner provides full text search of all packages in the database; this includes the compound name and synonyms and the abstract. Results appear as a list of packages with meta data. Use the Open link for each package to see the details.

Do not use the standard search for SMILES but use the chemical search instead.

A single word ("search term") such as

benzene

will return all entries containing benzene.

Multiple word queries such as

benzene methane

are interpreted as matching any of the terms. It is equivalent to searching for benzene OR methane.

Multiple words enclosed by double quotes as in

"benzene methane"

will only find packages that include exactly the phrase.

The "?" symbol stands for a single arbitrary letter, the "*" for multiple (0 or more) characters. Neither "?" nor "*" can be used as the first character of a word.

The search engine understands boolean operators (which must be written in ALL CAPS)

AND, &&

both search terms must be present

OR, ||

either of the terms must be present; OR is the default operator as described under multiple word queries.

NOT, !

the following term must not be included; the NOT operator cannot be used with a single term (use "-" for those cases).

+

A term prefixed with "+" must be included for a match.

-

A term prefixed with "-" must not be included for a match.

Parentheses can be used to group expressions:

(methane OR ethane) AND NOT octane

The following characters have special meaning in the search syntax:

+ - && || ! ( ) { } [ ] ^ " ~ * ? : \

In order to literally include one of these characters into a search query, you must escape the character by prefixing it with a backslash \. For example, to search for "(1,2)-dione" use

\(1,2\)\-dione

The search functionality uses the Apache Lucene search engine and hence the documentation of the Lucene query syntax applies.

One can restrict a query to search a specific database field. For instance,

matadata.name=benzene

will only show entries where the name field contains the word benzene; if it occurs only in e.g. the abstract then it will not be shown.

The following package field allows a unique package to be retrieved:

package.packageId:1

fetchs a unique package with id=1

The following metadata fields are currently defined:

metadata.abstract

user supplied abstract as free form text

metadata.ligandCode

3-letter code assigned to any protein ligand in the Protein Databank

metadata.name

name of the package on Ligandbook; typically a common name

metadata.otherNames

synonymous names, including commercial names

metadata.canonicalIUPACname

official systematic IUPAC name

metadata.pubchem

PubChem compound identifier (CID)

metadata.moleculeIdentifier

CSTS molecule HASH-id

The following additional fields are currently defined:

forcefield.name

Name of the force-field useg, e.g. CHARMM, OPLS-AA, Amber

code.name

Name of the force-field useg, e.g. CHARMM, OPLS-AA, Amber

packageId

Internal, permanent database ID (DBID/LigandbookId)

curator.username

User login name

curator.profile.truename

"True name" of the user