AMBITDatabase HELP

How to search in the database. (last revision - 14 June 2007)


Dataset

Specifies which dataset will be searched.

The user can select between the different datasets existing in the AMBIT database.
Subsequent searches will be performed only within the selected dataset.

Results output

Specifies where search results will appear.

  • The default option is a new list in Molecule browser, this means that results from previous queries will disappear.
  • The second option will forward the result again to the Molecule browser, but the old list will not disappear, only the currently displayed molecule will be replaced by newly found one.
  • The third option allows to redirect query results to a file. Thus, all search result will be stored in a user selected file. The file save dialog, allowing to specify the file, will popup when the search is initiated.
  • The database options allows to store the results as a new "named dataset", which will be available from the dataset menu above for further processing. 

Similarity method

Specifies which similarity method will be used by similarity search.

Fingerprints

Fingerprint similarity uses Tanimoto distance between 1024 hashed fingerprints generated by The Chemistry Development Kit, CDK class Fingerprinter. It follows the ideas of Daylight fingerprint theory, i.e.

  • for a given molecule all possible paths for a predefined length (default is 7) are generated,
  • the path is submitted to a hash function which uses it as a seed to a pseudo-random generator
  • the hash function outputs a set of bits
  • the set of bits thus produced is added (with a logical OR) to the fingerprint.

Atom environments

atom environments, circular fingerprints
Tanimoto coefficient on atom environments

Molecule processing options

Molecule processing options

There are number of actions applied to structures in the Molecule broswer. By default the actions are applied to the current structure. To apply the action to all structures in the Molecule broswer:


  • Use Search Options/Options  menu
  • Select Molecule processing tab  (picture at the left)
  • Select Molecule Browser: Current set of structures from the first list box

Developed (2006) by Joanna Jaworska and Nina Jeliazkova for CEFIC-LRI