Thursday, April 26, 2012

Some thoughts about ACS in San Diego

I attended the ACS a few times before, but this one was special. Not just because this time the meeting was held in San Diego (it was great to return to this beautiful city and meet some friends and colleagues I haven’t seen for a while), but even more importantly we announced the release of the beta version of mcule.com (go to mcule.com and enter your email address to get access). We put down the basics. Now the question was where to go from here. We certainly had a lot of ideas about where we could go, but we needed (and still need) some feedback from our future users on these plans. In general, feedback was positive about the beta version and people found some of our plans attractive. This is good.

People already tested mcule.com will probably see the difference from other chemical database hosting websites, but those who haven’t seen it yet were asking why are we different. So here is why:
1. First, we provide purchasable molecules AND screening tools. There are some services for either of the two individually, but such an integrated system of these two components makes mcule.com unique.
2. Data quality: we have spent several months developing a rigorous registration system yielding in a high quality database. These days, when large chemical and biological data are accessible, emphasis is placed on the quality rather than on the quantity of databases.
3. Top IT technology behind mcule.com allows many things that are not available anywhere else. For example, flexible collection management for millions of compounds is not a trivial task at all but it is possible on mcule.com.

Another very important feedback coming from many computational experts and non-experts was the following:

- You provide high quality, purchasable molecules. OK. And you will provide a bunch of searching/screening tools. Nice. Now, how will I know which tool is the best for a particular problem?

So it looks like providing a large haystack of molecules and different pitch forks might be attractive for experts, but even they want to know what the best tools for finding the needle are. Computational chemists especially working in the pharma industry simply don’t have time to make large-scale assessments of tools. Looks like we have to do this extra step. And we are happy to do that! So therefore, one of our primary focuses for the next few months is to build up automated screening workflows, optimized and validated by using reference molecules. We have already done this for a few case studies even with experimental validation. For example you can check out our ACS poster on GPCR fragment library selection with 100% hit rate. Such validated, preset workflows will be provided for our users. We will also allow automated validation of screening workflows on any target for which reference molecules are available to assess their predictive power. The ultimate goal is something like this: user goes to mcule.com, enters a target name and gets potential ligands coming out of a validated virtual screening workflow. We are working on it …

PS: You can find all our ACS presentations here.


  1. mcule have very interesting approach. What kind of virtual screening algorithm do you use?

  2. Hello Vladimir! The current private beta version contains algorithms for exact (simple), fingerprint based similarity and substructure searches. Physchem property filtering and docking (Autodock Vina) are the next things to implement. We have a few others in progress. Let us know what you would like to see and we try to prioritize accordingly!