Structure Searching

Databases for Chemical Structure Search
Apart from the well-known SciFinder database, free databases for chemical structure search are the following:

1) Pubchem. PubChem, released in 2004, provides information on the biological activities of small molecules. PubChem is organized as three linked databases within the NCBI’s Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links in the homepage.
Links from PubChem’s chemical structure records to other Entrez databases provide information on biological properties.

2) ChemSpider. ChemSpider is a free chemical structure database providing fast text and structure search access to over 28 million structures from hundreds of data sources.

3) ChemFrog. ChemFrog is a chemical database that offers over 1 million commercially available chemicals and vendor information.

4) ChemDB. ChemDB is the IGB Chemical Database: The most diverse and useful set of chemoinformatics tools and applications available to the public. Applications: Chemical Search Find a chemical by basic criteria like molecular weight and predicted logP, or by the more abstract notion of structural similarity. Virtual Chemical Space Interactively deconstruct target compounds into component precursors and reconstruct similar building-blocks into combinatorial libraries representing the “virtual chemical space” near the target compound. Reaction Explorer Interactive system for learning and practicing reactions, syntheses and mechanisms in organic chemistry, with advanced support for the automatic generation of random problems, curved-arrow mechanism diagrams, and inquiry-based learning. COSMOS Predicts 3D small molecule structures from various standard 2D formats Reaction Predictor Predicts Mechanistic Reactions Using Machine Learning.

5) iScienceSearch. An Internet search engine for chemists. iScienceSearch also supports mobile devices and it works well to draw structures on something like an iPad. We use JSDraw from Scilligence (www.scilligence.com) to draw chemical structures. This is a good application to find out for yourself if mobile devices are useful for research. Please remember to allow pop-ups otherwise you don’t see the result page. Links to tools that predict biological activities and many other parameters of a structure, like logP are incorporated. PASS (Prediction of Activity Spectra of Substances) (www.akosgmbh.de/pass) predicts with high accuracy about 4000 effects for a compound.

6) Chemicalize (www.chemicalize.org ) from ChemAxon calculates structure parameters.

7) The DistilBio (a powerful, federated, life sciences search engine) new release now has instant display of results. http://distilbio.com With instantaneous search results and auto-complete, it is now even easier to find the research you are looking for all in one place. Visit the site and try it with “Aspirin”.


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