Followers of the ChEMBL group's activities and this blog will be aware of our involvement in the migration of the previously commercially available SureChem chemistry patent system, to a new, free-for-all system, known as SureChEMBL. Today we are very pleased to announce that the migration process is complete and the SureChEMBL website is now online. SureChEMBL provides the research community with the ability to search the patent literature using Lucene-based keyword queries and, much more importantly, chemistry-based queries. If you are not familiar with SureChEMBL, we recommend you review the content of these earlier blogposts here and here . SureChEMBL is a live system, which is continuously extracting chemical entities from the patent literature. The time it takes for a new chemical in the patent literature to become searchable in the SureChEMBL system is 1-2 days (WO patents can sometimes take a bit longer due to an additional reprocessing step). At time of writi
The Organization of Drug Discovery Data
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You could also think of using descriptors that rely on a PCA analysis of the input data you are providing (actually I could help you with some of these, although in the form of a PP component).
We are mostly interested in bulk sequence properties at the moment (so fractional composition, hydrophobicity, features, etc), so a descriptor that gives a number for an input sequence.
There are loads of other stuff that would be cool to add, antigenicity, secondary structure prediction fractions, etc.
The sort of license issues are related to use of services which are freely available for academics, but there are some restrictions for "commercial use" - for example TMHMM http://www.cbs.dtu.dk/services/TMHMM/ where there is a download version of the software for academic institutes to use. I would guess that this license doesn't really cover the setup of a derivative service, allowing access over web services. This is just one example, not highlighted for any particular reason; but we would need to get permission from a fair number of software providers.
If we do set it up we want two things 1) freely accessible to all without restriction by user type and 2) compliant with the software licenses and wishes of the original authors.
http://nar.oxfordjournals.org/content/34/suppl_2/W32.full
the webserver is located here:
http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi
However I cannot tell you anything about the performance of this particular descriptor, might serve as a benchmark to your own solution?