Press Release Details


Santa Fe, NM, and Raleigh, NC, December 12th, 2007 – OpenEye Scientific Software, Inc., the developer of innovative molecular modeling and cheminformatics solutions for drug discovery, and ChemZoo, Inc., the provider of online chemistry software and services for the chemistry community, announced today they had entered into an agreement that will allow the incorporation of a number of OpenEye’s products into ChemZoo’s online chemistry database and property prediction service, ChemSpider.

OpenEye’s Lexichem has already been used to generate IUPAC names for compounds in the ChemSpider repository. In the future, Lexichem will also be used to convert IUPAC or other chemical names provided by users of the ChemSpider site into chemical structures in real time. Ogham will provide 2D depictions of chemical structures. Filter will calculate physicochemical properties for compounds in the ChemSpider repository, while Quacpac will allow the normalization of protomeric and tautomeric forms. Lastly, OEChem will be the engine behind the manipulation and conversion of standard molecule file formats.

“We are very pleased to contribute to ChemZoo’s vision of providing structure-based access to federated chemistry databases in a chemist-friendly environment via ChemSpider”, said Dr. Matthew Stahl, Senior Vice President of OpenEye Scientific Software, Inc. “We’ve allowed the academic community free access to our products for ten years, as we have continued our research towards better modeling and cheminformatics tools. This new partnership is fully in line with that philosophy: chemists from around the globe will now have free access to a central repository with efficient data-mining and rendering tools, partly powered by our technology. This is a great satisfaction for OpenEye.”

“The ChemSpider service presently offers chemists access to a database of nearly 18 million compounds with text and structure/substructure searching capabilities”, continued Dr. Antony Williams, Founder and President of ChemZoo, Inc. “The incorporation of OpenEye’s technologies will allow us to add important capabilities to both our transactional services as well as to enhance and improve the data within the ChemSpider repository. The ChemSpider service strives to become the foundation of an online chemical structure centric community for chemists. Chemists around the world can already add their own structures and analytical data to the database for public review and access. The near future will continue to enhance our collaborative and enabling environment for chemists.”

About OpenEye

OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts and Strasbourg, France. It was founded in 1997 to develop large-scale modeling applications and toolkits – programming libraries suitable for custom development. Primarily aimed towards drug discovery and design, areas of application include chemical informatics, structure generation, docking, shape comparison, charge & electrostatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye software is distributable across multiple processors, supports 64-bit processing, and runs on Linux, Windows and Mac OS X, as well as HP, IBM, SGI and SUN flavors of UNIX. For further information on the company and its products, see

About ChemZoo

ChemZoo, Inc., was founded with the intention of providing online chemistry software and services to help build a chemical structure centric community for chemists. Their first offering, ChemSpider, is a chemistry search engine built with the intention of aggregating and indexing chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. Founded in 2007 and located in Raleigh, North Carolina, ChemSpider intends to become a facilitator in the exchange of structure-based information between chemists worldwide. For further information, see

Contact information EXCLUDED so the spammers don’t adulterate us further…please post back if you want info…

Stumble it!

5 Responses to “ChemSpider to Incorporate More OpenEye Software: PRESS RELEASE”

  1. Egon Willighagen says:

    Amazing! (Forgive me that I read not read every bit…) But, amazing! A press release for the fact that one may use software ;)

  2. Jean-Claude Bradley says:

    Which physicochemical properties does this include?

  3. Antony Williams says:

    Egon, I’m reading sarcasm into your comment and I may be wrong and you’re just celebrating the fact that we have the software. If I’m misinterpreting then I apologize in advance.

    Yes I think it is amazing that companies of this caliber are willing to provide their tools at no cost to systems like ChemSpider. There have been a lot of attacks over the months on commercial companies, publishers etc and my position is that without a capitalistic society our western world would likely collapse. Companies like ChemAxon, OpenEye, ACD/Labs, SimBioSys (companies I know personally) do give a LOT of software, support, donations etc to academia and not for profits every year and are rarely acknowledged for their efforts. Probably Cambridgesoft, Accelrys, Symyx/MDL and so on do too. It is common for these companies to be treated with disdain for being in business. Not fair I say. The people in these companies work harder than most people I know, with the intention of paying their bills and taking care of their families just like the rest of us. It is their chosen career so why should they be beaten up for it? Many of our colleagues interested in the more Open aspect of the world coexist will a balance of openness and commercialism or support of commercial entities. Joerg Wegner has been vocal on this and suggested OpenEye as a partner for us. Rich Apodaca now has his own company, Metamolecular.

    The divisiveness in the chemistry software community between Open and Commercial needs to be managed and navigated but certainly standing on separate sides of the river is not helping to build community.

    I am happy to acknowledge that more and more companies are stepping up to help ChemSpider. Meanwhile, some of the advocates of Openness have remained judgmental of our efforts. It’s an interesting time.

  4. Antony Williams says:

    The list of physicochemical properties is yet to be resolved and will not be done until middle of first quarter next year. We have established the relationship now to provide access to certain capabilities which were removed and the relationship/capabilities will be expanded as we learn the software components and have enough bandwidth available to incorporate and calculate. I’ll keep everyone informed here on the blog.

    By the way, the reason that the functionality started to fail that you are interested in (batch deposition) was due to the fact that the OpenEye trial license expired on that day. I was testing the deposition system last night with a number of other people and can say it is ready to go for EVERYONE (single and batch structure deposition) as soon as we get the new license key from OE..probably today.

  5. Egon Willighagen says:

    I’m happy you can use their software, really. But isn’t just buying the software? If you buy the software you may use it, not? Sure the companies may protect their IP. That’s their business. OpenEye certainly has nice products, as there are many are excellent provindings. They are certainly way ahead of what I have access to.

    I’m sure some people can use it for free, but I am also sure that only a selected group really knows what is going on in the code.

    It’s just that I was reading from press releases like this, that ChemSpider should be happy that they may be using the software the way the want. And that sounds like the vendor is dictating what you may and may not do even after ChemSpider purchased the software. Seriously, license from chemoinfo industries can be really restrictive.

    I was actually a bit sarcastic about that situation, as I find it an absurd situation: to be have to annouce that you bought a product (well, *I* blogged about having a Wii too :) . Nothing about OpenEye, really; they have done amazing things, *and* even contributed to Open Source!

    My apologies for not being more clear in my previous comment.

Leave a Reply