CDD is moving offices

CDD is in a stage of growth, and we will be relocating our offices over the holiday period and opening our doors at a new location. Update your contact details with this new address: 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010. Come and visit with us a while and discuss our efforts to build the premier collaborative drug discovery software platform on the market!

We’re happy to announce the release of the latest version of CDD’s software, now available live at www.collaborativedrug.com. The big update in this release is the ability to archive information on scientific references (references as in the references section of a publication). There are two goals for this functionality: 1) to allow researchers to share lists of relevant articles with each other, and 2) to provide a convenient way to link back to the original article when curating data from literature. We have addressed the first goal with this release, and are now working on the second goal, which we plan to release soon.

With this release we’ve made it convenient to search PubMed for articles, and to then import the relevant ones into your private CDD database. You can also upload PDFs to share with colleagues in your private group (and only within your private group, which is permitted fair use of these often copyrighted materials).

A few other important fixes were also included in this release:

• (+), (-) and (+-) or (+,-) or (+/-) or (+ -) are now permitted in molecule names: This was a slightly embarrassing issue of overzealous molecule name canonicalization that caused problems for some users. You can rest easy now knowing that the name (+)-epinephrine is considered different from (-)-epinephrine by the CDD database.
• Both ChemAxon Extended SMILES and standard SMILES are now provided in Excel/SD exports. When exporting to Excel/SD file and remapping and slurping structures into CDD, always remember to use the ChemAxon Extended SMILES instead of standard SMILES. Standard SMILES is also provided if needed for other applications. Extended SMILES supports some annotations that standard SMILES does not, but MOL files do. For example, R-group labels in Markush structures, or relative versus absolute stereoconfiguration.
• We now check whether batch dates are valid dates when slurping. These will show up as errors in the QC report, instead of silently causing problems after you accept the report. So, for example, “NA” as a batch date is explicitly no longer accepted.

We hope you find the new functionality useful, and as always we welcome your feedback at support@collaborativedrug.com.

The number of contributers and datasets on the Collaborative Drug Discovery platform is increasing on an ongoing basis. Not only are our users adding to the content, both public and private but we ourselves continue to assemble databases to benefit the community. Most of our efforts will result in an increase in the Public Access datasets. The present list of Public Access datasets can be found here. Keep checking this page. More datasets will be showing up shortly.

We are all about Collaboration…it’s in our name! Since our databases sit on a growing foundation of small molecules and their potential contributions to drug discovery, it is natural that we would want to connect our structure collection to additional information that could be of value to our users. There are many open resources of structure-based content available on the internet. Some of those resources include PubChem, DrugBank, KEGG and many other databases. We want to focus our resources on developing the CDD software platform and partner with those resources providing the greatest value to our users so, when selecting a public  resource for providing additional information we chose ChemSpider.

ChemSpider is a free resource for chemists providing access to over 21 million unique chemical entities sourced from almost 150 data sources, many of these of value to drug discovery scientists. ChemSpider has already indexed PubChem, Wikipedia, DrugBank, PubChem and many other valuable resources. We don’t have to do that work. ChemSpider also actively curates and enhances the data on an ongoing basis using a crowdsourcing approach. We all benefit.

As an example of the linking between records the following integration path is shown below with the ChemSpider link highlighted. When this is selected you are taken directly to the ChemSpider record as shown below, in this case into the ChemSpider record here.

ChemSpider has a series of web services available that we might take further advantage of in the future. For now we are happy to connect across the web to the spider.

How many ways are there to communicate how something small can grow to become something much bigger…

Every long journey starts with a single step
Large Oaks from little acorns do grow
And maybe one for our era…  Today the financial sector, tomorrow the auto industry and next week ?

Well, let’s go with the large oaks analogy and talk about how it applies to Collaborative Drug Discovery. We established our company with the intention of making a real difference in the world. With a focus of helping drug discovery scientists around the world by delivering a software environment to archive, mine and collaborate we believe that we can make a real contribution to the process of discovery. We are proud of what we have been able to deliver using a very small team of committed and passionate individuals but we want to deliver more. In order to do so we are expanding our team, expanding our space and, over the next few months, you will see expand our reach in terms of collaborations and projects. In January 2009 we will be moving from our present offices and are now in the process of expanding our team. We are presently looking for a Community Support Professional and a Senior Software Developer as listed on our Jobs page. We are in an exciting phase of growth yet remain focused on our intention of delivering the premier software platform for collaborative drug discovery. Watch this space…