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.


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.

Basic queries

Single word

A single word ("search term") such as


will return all entries containing benzene.

Multiple words

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.

Boolean queries and grouping

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

Special characters

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


Advanced queries

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,

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:

fetchs a unique package with id=1

The following metadata fields are currently defined:

user supplied abstract as free form text
3-letter code assigned to any protein ligand in the Protein Databank
name of the package on Ligandbook; typically a common name
synonymous names, including commercial names
official systematic IUPAC name
PubChem compound identifier (CID)
CSTS molecule HASH-id

The following additional fields are currently defined:
Name of the force-field useg, e.g. CHARMM, OPLS-AA, Amber
Name of the force-field useg, e.g. CHARMM, OPLS-AA, Amber
Internal, permanent database ID (DBID/LigandbookId)
User login name
"True name" of the user