Molecular Craigslist
I think we need an eBay for molecules. Or maybe a Craigslist.
We’ve identified some potent new antimalarials in the open source drug discovery for malaria project that are already being investigated in vivo. The series seems interesting, and we may need to explore it fully if the biological results are good. We may need to make a bunch of analogs, but we don’t want to spend time making molecules that are commercially available. Iain Wallace has been doing some lovely analysis of which compounds similar to the new hits are commercially available.
I had a very interesting meeting at UCSF Mission Bay with John Irwin this morning which made me realize we ought to be using Zinc more. A quick search around our most potent hit threw up these commercial compounds, for example. We ought to check them out.
Given we can identify relevant, commercial compounds we now need to contact suppliers to see if they might donate.
But we can do more than that. What about compounds that might just be sitting in fridges in academic labs? A quick SciFinder search led us to this paper, and we’ve contacted the relevant group at Scripps to see if they might share some compounds.
But we can do more than that too. Imagine there is a group somewhere with expertise in making these kinds of compounds, and who might want to make some analogs as part of a student project, in return for collaboration and co-authorship? What about a Uni lab which might be interested in making these compounds as part of an undergrad lab course?
Wouldn’t it be good if we could post the structure of a molecule somewhere and have people bid on providing it? i.e. anyone can bid – commercial suppliers, donators, students?
Is there anything like this? Well, databases like Zinc and Pubchem can help in identifying commercial suppliers and papers/patents where groups have made related compounds, but there’s no tendering process where people can post molecules they want. Science Exchange has, I think, commercial suppliers, but not a facility to allow people to donate (I may be wrong), or people to volunteer to make compounds (rather than be listed as generic suppliers. Presumably the same goes for eMolecules, and Molport?
Is there a niche here for a light client that permits the process I’m talking about? Paste your Smiles, post the molecule, specifying a purpose (optional), timeframe, amount, type of analytical data needed, and let the bidding commence?
Benefits to this Molecular Craigslist are:
For Businesses: Business
For Donators: Good PR and possibly a collaboration
For Students/PIs/Synthetic Chemists: Possible collaboration and authorship.
Easy to make such a site?
mattoddchem, 
Intermolecular 
Chemjobber 8:26 am on April 20, 2012 Permalink |
I am not a chem-informatician, but I believe that the Available Chemicals Database is supposed to service a portion of this function. Problem is, of course, that just like Craiglist, the ACD has been spammed to death of recent years.
A company saying that they have a compound on the ACD is not the same as them actually having it.
mattoddchem 8:37 am on April 20, 2012 Permalink |
Right. My conception is needs-driven. If you *want* something you list it, rather than if you’re selling. And with Craigslist the site is not involved in the transaction, which is also good.
I should mention that another relevant site is Innocentive. That, to date, has been for larger competition-type requests, rather than micro-requests. There are rewards/incentives etc. And of course the site is involved in the transaction, with paperwork that allows secrecy in the dealings between the party that offers and those who want to solve. Craigslist keeps that to a miniumum by, at most, anonymizing emails. But it lets buyer and seller negotiate directly, with small transactions.
Chemjobber 9:11 am on April 20, 2012 Permalink |
Yeah, I’d be for it.
Mike 8:55 pm on April 20, 2012 Permalink |
This may (but in all likelihood not) be potentially suited to sites similar to Freelancer.com that really started out as a way to outsource (in a very cheap manner) relatively simple web design/logo design tasks. The categories on the site don’t really reflect a remotely chemical/biological basis (more categories at http://www.freelancer.com/sellers/) , but in part I’m sure that’s due to the fact that this probably hasn’t been trialled much.
It’s a start but I think the reward/incentive system would need tweaking for an academic context.
bill 2:05 am on April 21, 2012 Permalink |
Bioroot was an early attempt at something very like this. It died of neglect (not the developers’ — the potential users’).
mattoddchem 12:25 am on May 16, 2012 Permalink |
Chris Southan made a nice survey asking whether companies would be willing to get involved in supplying compounds to philanthropic projects:
http://www.surveymonkey.com/s/SXXZDX9
Dr. Alex M. Clark 9:29 am on May 24, 2012 Permalink |
Something like this might be quite a good fit for the Open Drug Discovery Teams (ODDT) app (http://molmatinf.com/products.html#oddt). The mechanism by which the server harvests chemical data originating from tweets with particular hash tags seems like it would provide a good fraction of the functionality up front – or at least enough to establish social proof, with more features added later if it catches on.
We could create a new topic called “Mat’s List” (#matslist)… or something a bit more general if you don’t feel like taking all the credit for it 🙂
sharing data, molecules and ideas openly – from a wealth of hits to none » Collaborative Chemistry 1:38 am on May 25, 2012 Permalink |
[…] were suggested and some very good comments made. This was initially described in the context of the open malaria work going on. Thinking about this it’s pretty applicable to the whole neglected and rare disease research […]
Paul Ylioja 11:40 am on May 28, 2012 Permalink |
Just read an old Nature article [http://dx.doi.org/10.1038/news040816-14] that mentions Eli Lilly’s internal drug candidate “Stock Exchange” for predicting which compounds are likely to make it to market. It would be nice to know more about their system. Is it still going?
Wolf-D. Ihlenfeldt 3:15 am on July 7, 2012 Permalink |
Why re-invent the wheel?
Innocentive (www.innocentive.com) provides the functionality requested, has been operating for many years, and built a reputation…
Alex Hoekstra 8:43 am on July 8, 2012 Permalink |
What about Assay Depot? It’s fundamentally like Amazon.com for science. You can contract research, chemical synthesis, reagents, supplies; compare prices; read and write ratings and reviews; browse catalogs and services; contact organizations directly…it’s pretty neat.
Companies and Open Science « Intermolecular 3:58 pm on September 25, 2012 Permalink |
[…] Comments Alex Hoekstra on Molecular CraigslistWolf-D. Ihlenfeldt on Molecular CraigslistPaul Ylioja on Molecular Craigslistsharing data, […]
Sean Seaver 3:35 pm on January 19, 2013 Permalink |
We get a lot of requests for products and the vast majority are fulfilled by locating items from existing sources. As you mentioned the Zinc database contains 28 million compounds and sorting through this information can be difficult and very time consuming for researchers. I wonder what would be the demand for a platform for requests, it’s certainly an interesting idea!
mattoddchem 9:40 pm on May 12, 2013 Permalink |
A related idea from John Irwin at UCSF – but again, people offer molecules, as opposed to someone posting what they need and asking for suggestions/collaborators.
http://zinc.docking.org/browse/catalogs/collabocules