My News and Views about Scaffold Hunter and Scaffold Tree appeared this week in Nature Chemical Biology.
The Wetzel paper on Scaffold Hunter is here:
If you haven't checked out this software yet, take a look. I am particularly happy that they GPL'd the code. http://scaffoldhunter.sourceforge.net/. Congratulations to Stefan and Co. !
We are making many improvements to DOCK Blaster. Recently, we introduced a new color-coded preliminary docking assessment table that aims to provide a yes/maybe/no answer to the question: Should I continue with docking. We thank the referees of our paper for prompting us to bring this forward.
Have you run a docking campaign, including purchasing compounds and testing them, only to find that nothing worked? What do you think went wrong? Do you think you could have done better if you had done things differently, or do you believe the project was doomed from the start?
I am interested in hearing from you. You can reply to this blog post, or you can write to me privately at jji at cgl dot ucsf dot edu. It does not have to be long. I am looking for stories of failure, with the aim of learning how to make docking better.
I hope to hear from you!
I am using the NPD for virtualscreening. I would like to purchase one of the compound from that database, but unfortunately the purchase info of that compound shows "Not for Sale". Can you pleas tell me how can I get that compound?
The Zinc ID is ZINC13393245
Waiting for reply,
Amrita School of Biotechnology
We are retiring the old versions of ZINC.
Versions 7, 6 and 5 are now all over two years old. Given the huge turnover in the chemical marketplace, we can think of no reason why anyone would want access to such old versions of the database.
Still, if you do need access to old versions of ZINC, please write us and we will do our best to help you.
New ZINC subsets appeared today, Wed Jul 8, 2009:
#33 - goldilocks - not too this, not too that. just right. Try this set if you are getting too many "extreme" molecules that you do not like (although, getting extreme molecules may point to an underlying problem with your docking model)
#26 - all-now - chemical space in under two weeks.
#37 - sarah - back by popular demand. purchasable compounds under 250 Daltons. that's it. suitable for the model system sites
Happy Canada Day to everyone!
We have some new subsets that appeared on the ZINC website today (Jul 1, 2009).
1. "leads now", subset 21. 2.18M compounds (was 1.96M)
2. "drugs now", subset 23. 6.28M compounds (was 5.67M)
3. "clean CNS permeable", subset 39. This is a new subset, and has 344K cmpds.
As always, we welcome your feedback about ZINC. Please don't hold back. Your comments help us fix problems that we either have not noticed or have let slide.
For people having outstanding issues to which I have not yet responded:
a) thanks for your patience
During May we have updated the following vendor catalogs in ZINC:
Aurora, BioBlocks, ChemDiv, ChemBridge, Enamine, Florida Heterocycles, IS-Pharm, KeyOrganics, Otava, Princeton, Shanghai Sinofluoro, TimTec, Vitas-M.
Hundreds of thousands of new compounds, and at least tens of thousands of depletions.
We have just exported fresh copies of all the "fragment" subsets. Coming up: "leads" subsets.
The "clean fragments" subset of ZINC, #12, was released today. It has 178K purchasable compounds, up from 126K in January 2009. "clean" ZINC subsets have stricter filtering rules applied to remove molecules that might not even be a problem. They are ideal for people who are willing to sacrifice a little chemical space coverage in return for a lower artifact rate.