CHEMOINFORMATICS TRENDS · An excess of proprietary databases lessens the attraction to open-source software
BY SALVATORE SALAMONE
October 14, 2004 | New offerings from Accelrys, LION bioscience, MDL, Synthematix, and Tripos may be the crest of a new wave of software designed to meet increasing demand to tightly incorporate chemoinformatics into the drug discovery process.
"The market for chemoinformatics tools is picking up, but it's not close to [that of] bioinformatics," says Judy Hanover, research analyst at Life Science Insights.
For years, chemoinformatics tools have lagged behind their bioinformatics counterparts. A study by Life Science Insights ("Leading Indicators in Life Sciences, March 2004: Basic Research and Drug Discovery") reported that about 35 percent of life science organizations surveyed have bioinformatics tools widely deployed in their organizations; only 15 percent indicated that chemoinformatics tools were in widespread use.
That's changing, and quickly. "Life science companies are getting to a point where pipelines are not there," Hanover says. "And there's a desperation to use tools like chemoinformatics to fill them."
The trend hasn't been missed by the vendor community. For example, LION loudly trumpeted the recent introduction of LeadNavigator, its first entry into chemoinformatics.
|Other New Tools
- Tripos recently announced SARNavigator 1.5, featuring SARNavigatorBASE, a chemical spreadsheet that can do chemical substructure searches.
- MDL introduced MDL Isentris, an out-of-the-box discovery informatics platform that supports both bio- and chemoinformatics activities and provides a way to integrate and share data between biologists and chemists.
- Synthematix added to Arthur 3.0, its flagship suite, new tools that allow integration with third-party applications and databases, including internal and public chemical substances databases.
LeadNavigator is a chemical spreadsheet that gives researchers the ability to pull together and visualize chemoinformatics data from many sources. LION developed the technology as part of a project started in 2000 for Bayer. Only now is LION turning it into a commercial product, spurred by growing demand. In fact, the chemical worksheet developed by LION is the main component of Bayer's PIx (Pharmacophore Informatics) platform. PIx gives Bayer researchers worldwide a single access point to all chemical data and tools.
The focus of PIx and likewise LeadNavigator on drug development chemistry versus general chemistry is regarded as a plus. "While regular chemical spreadsheets can partly solve this [data and tool integration] problem, the available solutions have not been well adapted for medicinal chemistry," says Hanno Wild, head of medicinal chemistry at Bayer HealthCare AG.
Most of the new tools can integrate data from a variety of sources. Open-source software has less of a stronghold on the market, in part because there are so many proprietary chemical databases, Hanover says.
Bioinformatics tools typically are used on public databases, which normally support common data structures (like XML) and use standard methods to access the data. By contrast, chemoinformatics tools rely more on proprietary (purchased by the company) or internally developed databases. Such databases often support proprietary data formats or access methods.
Some industry experts believe this difference in the type of data is another reason for the growing interest in commercial chemoinformatics software. Biotech companies are looking for help integrating and accessing these proprietary chemical databases into existing analysis applications.
The integration does not have to be at the platform level. For instance, Accelrys and GenSys Software recently announced a collaboration in which Accelrys' Accord Chemistry Control software will be used within GenSys' Electronic Laboratory Notebook to handle depiction of chemical data.