Associate Professor of Chemistry at Drexel University - Open Notebook Science advocate - drug discovery, malaria, organic synthesis, non-aqueous solubility
Anna - yes cost is an important consideration. But currently there is no free true substitute for SciFinder and Beilstein and I was pleased to see how CAS takes curation seriously. Over the next few years I think the quality of free databases will start to rival the commercial solutions though. Even now you could do a lot of good research without these tools but you are much more likely to miss some important papers and have to be careful.
- Jean-Claude Bradley
yes, just read the article and was quite impressed with their response. However, since we no longer afford CAS or Scifinder at our university, its all a bit irrelevant to us. They can be proactive, but I will never see it. And trust me, we are highly aware of the risks, but we have to negotiate with non-scientists on this one, who don't see scientific credibility as an issue. :(
- Anna Croft
Anna - that is interesting and another powerful reason for publishing OA - so that your articles will be found by your peers. Does anyone have stats on what percentage of PhD granting institutions have a subscription to SciFinder?
- Jean-Claude Bradley
Right Richard - Google Reader thought it was new :) As Cameron has said it doesn't hurt to have the odd long timescale loop on FF - if only for some of the new people joining
- Jean-Claude Bradley
This is the lecture from the 8th Chemical Information Retrieval class at Drexel University on November 12, 2009. It starts with a demonstration of how to use of ChemSketch and Chemspider to display and manipulate chemical structures, especially those with complicated stereochemistry. Technical issues with using SMILES between the two platforms are addressed, as are optimization of 3D structures and inverting chiral centers. Microsoft Paint is used to process screen captures to images that can be uploaded to Wikispaces. ChemSpider is also used to generate predicted properties. SDBS is used to retrieve NMR and other spectroscopic data.
- Jean-Claude Bradley
Mel Reichman, senior investigator and director of the LIMR Chemical Genomics Center at the Lankenau Institute for Medical Research presents at the chemistry department at Drexel University on November 12, 2009. Introduction by Jean-Claude Bradley. Modern drug discovery by high-throughput screening (HTS) begins with testing hundreds of thousands of compounds in biological assays. The confirmed hit rate for typical HTS is less than 0.5%; therefore, 99.5% of the costs of HTS are for generating null data. Orthogonal convolution of compound libraries (OCL) is 500% more efficient than present HTS practice. The OCL method combines 10 compounds per well. An advantage of this method is that each compound is represented twice in two separately arrayed pools. The potential for the approach to better enable academic centers of excellence to validate medicinally relevant biological targets is discussed.
- Jean-Claude Bradley
Mel Reichman gave an outstanding presentation at Drexel on November 12, 2009. I think many of our faculty and students benefited from his unique perspective on high throughput drug discovery and the story of Vioxx from both chemistry and intellectual property considerations. Screencast and slides available here.
- Jean-Claude Bradley
Our paper on Chemistry in Second Life is marked as "Highly Accessed" in Chemistry Central Journal - that's nice to discover http://www.journal.chemistryce...
I found the premise of Barbara Bradley Hagerty's new book "Fingerprints of God" quite intriguing. The author, raised as a Christian Scientist, attempts to look into alternative religions and science to see if her faith is justified. There is nothing really new here - in terms of topics that have been covered in many other popular books. But what I found interesting was her interpretation of her experiences and investigations. She chronicles her struggles and revelations in an autobiographical format - and I'm usually a sucker for autobiographies. read more
- Jean-Claude Bradley
Polymers are where the problem with assuming that chemistry is structure centric come home to roost of course. Nico Adams has been looking at developing ways of describing polymers effectively and it really isn't straightforward. The whole notion of substance, chemical, and structure get very very messy.
- Cameron Neylon
What is distressing is that someone added that initial obviously incorrect SMILES and it propagated easily to all those databases. As Tony has said many times curation is a big challenge in chemical databases.
- Jean-Claude Bradley
I'd say the cause of everyone blindly copying data, is that they are happy enough to be able to copy data at all... it all starts with Open Data and the right to fix things, and share those fixes...
- Egon Willighagen
I'm not sure that the reason people are copying data are because it's Open. PubChem continues to proliferate yet it is NOT Open. We've had this exchange before..PubChem is NOT Open data but I "judge" it gets copied because people treat it as an authority. It is not a good idea to treat PubCHem as an authority as it is a repository...non-curated and with no efforts underway to curate it...
more...
- Antony Williams
I agree that PubChem should not be treated as authoritative, but the big advantage it has over ChemSpider is that it can be downloaded and re-used.
- Michael Kuhn
I agree that people copying PubChem is indeed not because it is Open... that one is copied merely because it is free and confuse that with Open. That said, I love to see the day that there was a court ruling on that state of the PubChem data, which is at some places claimed to be Public Domain, something refering to the copyright being with the providers, while at other places... a bullet proof statement would be *very* useful indeed.
- Egon Willighagen
Michael - there is every intention to provide access to the ChemSpider structure collection in the near future. This will not include all associated information in a record as the associated information has mixed licensing but free to use.
- Antony Williams
ChemSpider and Wikipedia have the advantage that errors can be corrected. Are there mechanisms in place to correct errors in DrugBank, PubChem and the many other derivative databases?
- Jean-Claude Bradley
DrugBank: yes, David Wishart is said to be quite responsive to comments. Same for KEGG. PubChem: NO. They just aggregate tons of source databases, and you would have to hunt down the source and hope it makes it way downstream... Thus ChemSpider's annotation efforts are invaluable, and I would love to be able to re-use them
- Michael Kuhn
Michael...drop me an email at antonyDOTwilliamsATchemspiderDOTcom and let's discuss how you want to use information and what you need to get at and it might be an issue of simply pointing you to the right web services. Lots of people are using ChemSPider through web services at present. We'd love to help you
- Antony Williams
Interesting. This was bound to happen eventually. It's "Friendfeed for scientists", except that it's a little cluttered and hard to find your way around.
- Mr. Gunn
Prediction of solubility of drugs and other compounds in organic solvents - recent article by Abraham on non-aqueous solubility prediction - thanks Andy http://dx.doi.org/10...