Monday, October 29, 2007

Drug Design on the Open Web

A few months ago I started working with Mesa Analytics and Computing as a consultant on an SBIR project aiming to provide new tools for drug design. Although the business model component is confidential, a large part of the project involves the use and creation of freely available online tools for educational or other purposes.

This is a great example of a for-profit company aiming to provide significant value in the form of free services for the chemistry and biology communities. ChemSpider is another example.

What we would like to do is provide an intuitive interface for someone to perform some QSAR and docking work.

Mitch Chapman has provided a detailed description of a test dataset we'll use for the QSAR example. The advantage of using this source is that Rajarshi Guha has already created a publicly available service that we can use for performance comparison.

We are updating a "working scenario" to think about how this could all work and identify which pieces are missing. Hopefully we can put together a prototype for Phase I and find the right partners to get something robust constructed during Phase II.

This is all taking place on the UsefulChem wiki and we welcome contributions and suggestions from everyone.

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At 6:10 PM, Blogger Rajarshi said...

You might also be interested in a set of general stats web services that I've built. Given that they are web services, one needs to write a client interface.

Thus for example, there is a web service that does feature selection and a very simple client interface is at

Another example is automatically generating models from a set of descriptors and an observed variable. This is also avalable as a web service and a simplistic client front end is at

These are relatively complex services, but there are also services for more atomic operations (such as building an OLS model or CNN model etc)

Now, one might do these jobs with more flexibility locally, but if the aim is to develop an online resource, the R web services provide a way to plug things together pretty easily (well, if you know Python and SOAP, or Java or Perl or PHP :)

At 9:03 AM, Blogger Jean-Claude Bradley said...

Thanks for those suggestions!
This looks like the type of thing we are looking for.

At 1:31 PM, Anonymous Anonymous said...

you may be interested in the following review by Ertl and Jelfs

Designing Drugs on the Internet? Free Web Tools and Services Supporting Medicinal Chemistry
Curr. Top. Med. Chem. 7, 1491-1501, 2007


At 12:19 PM, Blogger Jean-Claude Bradley said...

Sven - thanks for the suggestion -this is very helpful!

At 5:13 PM, Blogger Unknown said...

Thanks @Anonymous for the paper suggestion, this is very interesting !

At 8:43 AM, Blogger Jean-Claude Bradley said...

It really is an interesting paper - too bad it is not from an Open Access journal :)
Ironic given the content...

At 4:35 AM, Anonymous Anonymous said...

The title of this post is suggestive of something I've written about briefly on ChemSpy, the notion of open access drugs


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