Zusammen

For practicing research chemists, a comprehensive and up-to-date source for information on commercially-available compounds is essential. Today's installment of our ongoing series on free chemistry databases and Web services takes us to eMolecules. From the about page:

eMolecules is the world’s most comprehensive openly accessible search engine for chemical structures. Each day, over 2,000 chemistry professionals visit our web site to find valuable information that helps them do their work more productively.

eMolecules is organized around the concept of a commercially-available small molecule. Records summarizing these entities can be found through two convenient methods: by structure and by text. eMolecules - the company - also offers a variety of services related to their database. One such service, eMolecules Plus enables research organizations to offer the eMolecules database with pricing information within the security of their own intranet. Very recently, eMolecules began offering the ability to download the entire compound dataset in a variety of formats.

Although many aspects of the eMolecules service are noteworthy, two of the most important are size and speed. With approximately 8 million structures, eMolecules hosts one of the world's largest public-facing collections of chemical structures. Unlike many large chemical structure databases available on the Web today, substructure search on eMolecules is fast - very fast. Queries returning tens of thousands of hits routinely execute in less than three seconds. The underlying search technology has been the subject of at least one patent application.

The eMolecules structure search capability is easily identifiable through the prominent placement of a chemical structure editor on the home page itself. The search interface is both powerful and intuitive. For example, positions on either carbons or heteroatoms can be "blocked" by using explicit hydrogen atoms to fill valencies. By drawing benzaldehyde with a hydrogen attached to the carbonyl carbon, my search only returns aldehydes - not acids, esters or amides.

Text-based searches recognize fields include CAS Number, IUPAC Name, and SMILES string.

For information on commercially-available small molecules, eMolecules is an excellent first stop. Those interested in keeping up-to-date with with latest can subscribe to the eMolecules blog.

Disclosure: eMolecules is a customer of Metamolecular, LLC, owner of Zusammen.

Kudos

• Incredibly fast substructure search.
• Prominent placement of search elements on home page.
• Freely-downloadable set of 2D and 3D structures.
• Focussed, well-thought design.

Ideas for Improvement

• After selecting a single vendor to search by, it's not clear how to deselect to view results from all suppliers. The result is that the eMolecules compound collection appears much smaller than it is with little indication of what's happening.
• Enable the inclusion of structures in feedback form.
• Add blog feed to front page.
• Prominently-displayed exact count of the number of molecules hosted.
• New molecules RSS feeds. Even better - user-configurable feeds that filter by substructure.