About CASPeR


What is CASPeR?

The Compounds Australia Structure PoRtal is a web portal delivering real-time structure information on the Compounds Australia Open Access Collections.

The portal will deliver information directly to the researchers by providing:

  1. Individual chemical properties
  2. Compound structures (provided approval has been obtained from the depositing chemist)
  3. Structure searching capabilities
  4. Up-to-date library numbers

Compounds Australia stores physicochemical information and hashed molecular fingerprints for Open Access compounds, generated as part of the compound registration process. A compound chemical profile is generated by Compounds Australia Structural Profiler (Profiler); a software component of the Compounds Australia Registration Proforma tool. Profiler was written using opensource cheminformatics libraries and is distributed free-of-charge to all sample depositors.

CASPeR will allow the user to Browse and Search the Open Access libraries and then export the filtered or desired compounds via PDF, CSV and Excel formats.

Browse Browse »

Browse the available Open Access library and filter the collection by chemical properties and library types.

Search the Open Access library using the SMILES string of a known compound or by drawing the compound in the interface provided. Two simple searching workflows have been utilised within CASPeR.

Two simple searching workflows have been utilised within CASPeR.

  1. Substructure - Searching for molecules containing specific query structures, and

    Substructure searching will identify compounds in the Open Access libraries containing the same structural fingerprint as the query molecule. In general, the structures found by this search will contain the exact query molecule, that is, they are superstructures of the query molecule. However, the results may contain a small number of false positive matches as a consequence of only comparing structural fingerprints rather than the actual structures, which are not available for all compounds in the Open Access library. In our internal testing, the number of false positive matches should be minimal (or non-existent) for most queries due to the length of the structural fingerprints implemented by Compounds Australia.

  2. Similarity - Searching for molecules similar (as a whole) to the requested structure.

    Similarity searching is useful to identify structurally similar molecules within the Compounds Australia collection that may display similar biological activity to a known molecule, that is, a query molecule. The search will identify Open Access compounds using industry-standard similarity criteria (tanimoto similarity >0.7 using path-based fingerprints). This workflow is not recommended for queries where full or partial exact matches are required (e.g. substructure search) or where the query structure and desired compounds are very different sizes, that is, the query drawn is only a small fragment of a biologically active molecule.


Open Access Libraries

There are 3 open access libraries on offer at Compounds Australia. These are:

  1. Open Access Academic library
  2. Open Access Scaffold library
  3. Open Access Drug library

Open Access Academic Library

Approximately 20,000 compounds submitted by Australian academic chemists and CSIRO are available for screening to national and international access members. Chemical property information of the Academic library can be obtained and filtered via CASPeR's Browse window. Structures are unavailable for the majority of the Academic library. Substructure and/or similarity searching are available via the compounds stored chemical fingerprint. Search the Academic library and identify your next collaborator.

The IP of the compound belongs to the chemist as the depositor of the sample. Following screening of the academic collection, researchers would communicate to Compounds Australia there interest in certain compounds and Compounds Australia would contact the depositors of the samples to follow up directly with you. In this case, Compounds Australia acts as the match maker only.

Open Access Scaffold Library

Compounds Australia has purchased a collection of 34,000 compounds focused on 1200 unique "scaffolds", delivering a diverse drug and lead-like collection of compounds available for biological screening. When an inhibitory compound is identified, follow-up screening to generate meaningful structure-activity relationships is possible as there are on average of 28 compounds per scaffold available (library size is ~34,000 compounds in total). Browse the Scaffold library structures or Search the Scaffold collection for a known or similar compound.

Open Access Drug Library

Compounds Australia has recently solubilised a purchased FDA drug approved library. This library is available in quantities <1uL and makes an excellent resource for target validation and identification screening, assay development. Browse the Open Access Drug library structures or Search the Open Access Drug library for a known or similar compound.


Contribution

Compounds Australia would like to acknowledge Dr Marc Campitelli (former Griffith University) for his contribution with all things cheminformatics. This includes generating the Compounds Australia Structural Profiler (Profiler) tool and designing the KNIME workflows for powering CASPeR’s search capabilities. Thank you Marc.