SureChEMBL
beta
Open Patent Data
Help & Support
  • Login

Structure search types

Index ↩

There are several approaches to locating chemical structures within patent documents. SureChEMBL focuses on the four most popular methods.

By definition, the examined molecule within a patent is called a target, the structure we seek is called a query, and a target molecule matching the query structure is called a hit.

The following chemical searches are available:

Search typeDescription

Substructure

Chemists are most often interested in Substructure search, that is, whether a target structure contains the query structure within it.

Note: If special molecular features are present on the query (eg. stereochemistry, charge, etc.), only those targets containing the feature are considered hits. However, if a feature is missing from the query, it is not checked and targets without that feature may appear as hits.

Similarity

A Similarity structure search looks for target structures that are similar to the query structure. The similarity concept implemented is based on hashed binary chemical fingerprints derived using a Tanimoto metric. That is to say, the presence of molecular features are recorded for both the query and the target and then compared using a standard formula.

Note: See Tanimoto Coefficient and Fingerprint Generation for a complete description of the concept and method.

Note: If you choose Similarity as your search type, you will be prompted to provide a Tanimoto coefficient between 0.5 and 0.95.

Major Match A Major Match structure search finds molecules that are equal in size to the query structure with additional fragments or heavy atoms allowed. This search type is useful to perform as it ignores the presence of salts or solvents beside the main structure in the target.
Basic A Basic structure search finds molecules that are equal (in size) to the query structure. No additional fragments or heavy atoms are allowed. By default, molecular features are evaluated the same way as described above for substructure search.
Identical In an Identical structure search, all molecular features need to be equal (e.g. a non-stereo query will only match a non-stereo target).
 

Other 'Chemical Searching' articles

Sorted by view count

  • Insert a SMILES, SMARTS, MOL, or Name Entry
  • Structure search types
  • Tanimoto Coefficient and Fingerprint Generation
  • Search type differences
  • Filter by molecular weight
  • Search for structure in doc section(s)
  • Structure drawing tool basics
  • Non MedChem-Friendly SMARTS
  • Support
  • Contact Us
  • The ChEMBL-og blog
  • @SureChEMBL on Twitter
  • SureChEMBL Webinar Part 1 Part 2
  • Technology Partners
  • Terms and Conditions
  • Cookie and Privacy Policy
  • Downloads
  • The ChEMBL database
The European Bioinformatics Institute

©EMBL-EBI 2014 | EBI is an outstation of the European Molecular Biology Laboratory

SureChEMBL is a trademark of EMBL

Funding for SureChEMBL is provided by Wellcome Trust, Open PHACTS, NIH and EMBL