What is it about?
The availability of structures and linked bioactivity data in databases is powerfully enabling for drug discovery and chemical biology. We review some of the issues with the divergent expansions of public and commercial sources of chemical structures.
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Why is it important?
We address a range of issues raised by the challenges faced resolving a series of "probe compounds" from the National Institutes of Health. We also highlight the confounding of prior-art searching by virtual compounds which could impact the composition of matter patentability of a new medicinal chemistry lead. Finally, we propose some potential solutions
Perspectives
See blogposts http://cdsouthan.blogspot.se/2014/11/pmid-25415348-back-story-on-bioactivity.html http://cdsouthan.blogspot.se/2015/03/a-look-at-infamous-goldfarb-patent-in.html
Dr Christopher Southan
This paper came about as we were working on the J Chem Inf Model paper on using Bayesian models of chemistry quality decisions on the NIH chemical probes. Chris made an observation on a mega patent and the challenges we saw as the commercial and proprietary databases diverged. I felt that was a great opportunity to also bring in the perspectives of Chris, Tony and Alex who are all concerned about chemistry data quality and accessibility.
Dr Sean Ekins
Collaborations in Chemistry
Read the Original
This page is a summary of: Parallel Worlds of Public and Commercial Bioactive Chemistry Data, Journal of Medicinal Chemistry, December 2014, American Chemical Society (ACS),
DOI: 10.1021/jm5011308.
You can read the full text:
Resources
NIH probe molecules in the Approved Drugs app
The NIH probe molecules discussed in the article have been incorporated into the latest version of the Approved Drugs app from Alex Clark
Blogpost: PMID 25415348 back-story on bioactivity dbs
Includes updated statistics and links from the paper
Predictions of an expert’s evaluation of the NIH chemical probes
A presentation from the in silico drug discovery conference, Dec 3rd 2014, RTP, NC. describes the analysis of NIH probes, machine learning and predictions
Our Disorganized Piles of Chemical Information
A blog post by Derek Lowe regarding this publication... "There are several points made. For one, there is far more publicly available information than ever before, and its total looks to outstrip the proprietary databases (such as CAS/SciFinder). The commercial databases, though, have the advantage of much better curation, and they remain far better for doing freedom-to-operate type searches on potential chemical matter."
CAS indexing of prophetic substances -example of megapatents, possible implications for chemical patent searching
Comments by Aleksandr Belinskiy about Paul Peters (CAS) discussing CAS recent practice of indexing prophetic compounds from patents, included the following slide in his presentation at the forthcoming EPO Patent Information Conference in Biarritz, France (Nov. 3-5, 2009).
A look at the infamous Goldfarb patent in SciFinder by CHris Southan
Chris Southan blogs about the detail that we had when we wrote the paper. Chris notes specifically "A key IP fact to note is that the deposition date of the 12 of August is before the patent priority filling date of 21st of December 2007. Therfore, as patenting after public disclosure, the claims can only be upheld in the US, since the PubChem results would be considered prior art in the rest of the world."
letter CAS sent to J Med Chem
Letter from CAS to J MED CHEM editor which was sent to me 20 Feb 2015..because they disagreed with the number we quoted in the paper, which 2 independent experienced SciFinder users came up with in mid 2014. Note paper published online Dec 4 2014 so CAS has had months to update this information.
letter from editor
And here is the letter from the editor.
Bio <-> Chem blog
More detail about the indexing of the Goldfarb patent, US20090163545 and substance linkages in SciFinder
Contributors
The following have contributed to this page
