Hopping for success

Molecular scaffold is a fundamental concept in medicinal chemistry. Perhaps nowhere this is more apparent than during early stage discovery, where scaffolds are the primary means by which medicinal chemists communicate. Extending this concept further, we recently introduced Scaffold Hopper as a tool that utilizes scaffolds to facilitate context “hopping.” Starting with either (i) a set of structures (e.g., hits from an HTS screening campaign), (ii) publication, or (iii) search terms, Scaffold Hopper allows the user to quickly “hop” between related contexts (i.e., compounds, documents, targets, MeSH terms) with just a single click. (We’re currently working to add additional contexts such as assays, clinical trials, and patents.) Below is a quick preview of the tool

Click on the Launch button below to take it out for a spin:


Note for Mac users: Due to recent Java security updates, Java webstart is no longer launched when clicking on the jnlp file. You can still launch it manually by select “Open With” then “Java Web Start” on the downloaded hopper.jnlp file. Please drop us a note if you have any problems.

A quick note on the implementation. We’ve made efforts to ensure that Scaffold Hopper can be run within the Java sandbox. While this provides some sense of security, it does mean that feature such as cut & paste (except only within tool itself) is not available. As always, we’d love to hear comments and feedback on how to improve the tool.

1 Comment

kfowlerApril 29th, 2013 at 3:16 pm

I found this quite useful for viewing the results of a ZINCPharmer query which returned >2,000 hits. I was able to quickly pick out scaffolds which differed from my query. I imported the top scaffolds into Cresset’s free TorchLite and and compared the fields of my query and the selected scaffolds.
I like the references that pop up for the scaffolds – a huge time saver!
I’m looking forward to copy/export functions, esp of the R-group table. Also, a delete scaffold function would be nice for R-group customization.
Keep up the good work!

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