Extending InChI Stereochemistry

Rich Apodaca — Wed, 09 Jul 2008 10:18:00 +0000

As covered by Reuters and many other wire services, ArtusLabs and Boston University's CMLD have teamed up to extend InChI's stereochemistry support:

DURHAM, N.C.--(Business Wire)-- ArtusLabs, Inc., a leading provider of life science software tools and data management solutions, has entered into a partnership with Boston University's Center for Chemical Methodology and Library Development (CMLD) to develop a way to standardize and expand the way in which stereochemistry, and ultimately a three-dimensional structures, are represented in the International Chemical Identifier (InChI(TM)).

With the increasing use of molecules containing axial chirality , planar chirality and other forms of non-tetrahedral stereogenicity in chemistry, the move by ArtusLabs and CMLD could be significant.

Put simply, the ability of cheminformatics to represent certain kinds of compounds has fallen way behind the ability of chemistry to make them. While molecules once considered mere oddities 30 years ago continue to pour into corporate compound collections, laboratory notebooks, and product catalogs, cheminformatics has been stuck with a form of molecular representation that hasn't changed significantly in several decades.

InChI isn't alone. All three of the most widely-used molecular representation systems now in use (Molfile, SMILES, and CML) suffer from fundamental limitations in representing axial chirality, planar chirality, and multicenter bonding.

The kind of work being undertaken by ArtusLabs and CMLD is essential if cheminformatics is to continue to keep pace with new developments in chemistry.

Yet Another Free Chemical Database: Reaction Searching with CMLD-BU

Rich Apodaca — Mon, 18 Jun 2007 09:08:00 +0000

As chemical informatics continues its climb out of a decades-long stagnation, the number of free chemical databases continues to grow. But despite all the activity, reaction databases are notably under-represented. For this reason, I was delighted to stumble onto Boston University's Center for Chemical Methodology and Library Development Reaction Database (CMLD-BU).

According to their website, CMLD-BU:

...is a new center funded by the National Institute of General Medical Sciences ( NIGMS ) focused on the discovery of new methodologies to produce novel chemical libraries of unprecedented complexity for biological screening. The goal of the CMLD-BU is to explore and expand the diversity of small-molecule libraries by creating general, useful protocols for stereocontrolled synthesis. ... A major objective of the CMLD-BU is also to provide information and chemistry protocols to the public on parallel and chemical library synthesis. ...

Use this link to begin exploring their service. To date the CMLD-BU has deposited just over 1,600 Substances with PubChem and their site shows 125 reaction protocols.

Although CMLD-BU's user interface could use some tweaking, their content is right on the money: real examples of preparative reactions with links to the primary literature and even spectral data.

Are we at the end of this process or at the beginning? Only time will tell. But the nearly infinite shelflife and ubiquity of chemical information coupled with the inexorable approach of virtually zero-cost computer services leaves only one of those two possibilities worthy of serious consideration.

Depth-First: Tag cmld

Extending InChI Stereochemistry

Yet Another Free Chemical Database: Reaction Searching with CMLD-BU