Thursday, February 21, 2013

Growing Beyond 1-Click Docking

In this post, we'll show you how to go just one small step beyond our 1-Click Docking tool, and how this is actually a giant leap for your productivity.

If you're using our 1-Click Docking feature, you already know how simple and quick it is to get a first insight into about a ligand-target interaction and affinity: just draw in a ligand, select a target and push a button: within 60 seconds you are presented with your results. But what happens if you want to do a bit more than that, refine some parameters, dock more than one ligand in one go, customize the binding center or save your results permanently? You can do all this and more, although it might take two, or even three clicks (but not much more!), after a free signup.

The Workflow Builder follows the same flow as the 1-Click tools: there's an input, we do some processing and save it to an output. By default, the input is set to the Purchasable compounds collection, containing more than 4 million unique, purchasable compounds that have gone through our rigorous registration system, but you can also use your own collection of molecules, either by uploading an SDF file, or by drawing in a molecule, just as you did with the 1-Click tools:

The first benefit of using Workflow Builder is that since we're using a Collection as input, we can dock more than a single molecule after one another into the same target automatically.
The meat of a  "Two-Click" docking workflow contains a single Docking (Vina) filter, which is unsurprisingly similar to the 1-Click version, but with a few more parameters you can set:
As opposed to 1-Click Docking, where your results are ephemeral, a Workflow's results are themselves saved to a Collection, whose name we can specify:
And after pushing the Run button, we get our results, just as with 1-Click Docking. The difference is that these results are not only stored for your future reference, but can also be used as an input for your next workflow.

As a free registered user of mcule.com, you can dock 500 molecules each month for free. If you get the taste for docking, you can sign up for a 100k package.

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