www.guidetopharmacology.org Looking at the gift horse: pros and cons of patent- extracted structures in PubChem Christopher Southan, IUPHAR/BPS Guide to PHARMACOLOGY, Centre for Integrative Physiology, University of Edinburgh. ICIC Heidelberg, Monday 23 rd Oct 2017 1 22 million
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Pros and cons of patent-extracted structures in PubChem
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www.guidetopharmacology.org
Looking at the gift horse: pros and cons of patent-
extracted structures in PubChem
Christopher Southan, IUPHAR/BPS Guide to PHARMACOLOGY, Centre for Integrative
Physiology, University of Edinburgh. ICIC Heidelberg, Monday 23rd Oct 2017
1
22 million
Abstract (will be skipped for the presentation)
2
As of August 2017, the major automated patent chemistry extractions (in ascending size,
NextMove, SCRIPDB, IBM and SureChEMBL) are included submitters for 21.5 million CIDs from
the PubChem total of 93.8. The following aspects will be expanded in this presentation, starting
with advantages; a) while the relative coverage between open and commercial sources is difficult
to determine (PMID 26457120) it is clear that the majority of patent-exemplified structures of
medicinal chemistry interest (i.e. from C07 plus A61) are now in PubChem b) this allows most
first-filings of lead series and clinical candidates to be tracked d) the PubChem tool box has
query, analysis, clustering and linking features difficult to match in commercial sources, e) many
structures can be associated with bioactivity data f) connections between manually curated
papers and patents can be made via the 0.48 million CID intersects with ChEMBL. However,
looking more closely also indicates disadvantages; a) extraction coverage is compromised by
dense image tables and poor OCR quality of WO documents, b) SureChEMBL is the only major
open pipeline continuously running in situ but has a PubChem updating lag, c) automated