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.

Saturday, February 2, 2013

Introducing our new design

You might have noticed that mcule started looking a bit different (frankly, much better) in the last few days. To reflect the fact that we are no longer in beta, we've decided that our design needed to grow up as well. There are still some pieces that need to fall in place, and of course, we are continuously improving mcule, but we are excited to introduce the new site and show you some of the biggest improvements we've made.

The new Dashboard

When you are logged in, the first page you'll see from now on is the Dashboard. From here you'll be able to quickly access all areas of mcule: the 1-Click Applications, your recent Collections and search results as well as predefined Workflow templates you can use as jumping off points.

Restructured navigation

We've given more descriptive names to our Search and Screen features. From now on, you will be able to make simple Exact, Similarity and Substructure searches on the Find Chemicals page. The Workflow Builder is the new, more descriptive name for what was previously somewhat opaquely called Screen. We've moved their links around on the top navigation bar as well.

Pre-defined Workflows

We've added three workflow templates that are accessible from the Dashboard to help you get started using the Workflow Builder. Each template is usable by itself, but really, they are meant to show you how you can use our filters to achieve various tasks. Feel free to experiment!

Workflows now flow

We’ve split the form we’ve used previously into two, so it’s easier to see what the input and output is in the Workflow Builder. Sounds like a minor change, but we think it greatly clarifies how to better use this feature. For example, did you know that you can use any previous workflow's result as the input for the next one? T

Simplified input

If you just want to paste an InChI or a SMILES, why waste your time fiddling with the sketcher? Or, if you’d like to draw in your molecule, why would you need any other fields? Input is now quicker and easier, not to mention less confusing.

All the small things

Fixing the bug that's been bothering us for days or adding a small button to a page in just the right place is unlikely to make the headlines, but nevertheless they are important. Who knows, maybe you bumped into one of them and you'll be glad to know that it's fixed, or that it's there. We've collected some of the smaller but no less important changes we've made:

  • You can upload molecules directly when creating a new collection
  • When viewing a docking pose, the view is rotated around the docked ligand
  • When viewing a docking pose, the docking target's name brings you directly to the target's index page
  • Fixed issues with unnecessarily added or missing bonds in GLmol
  • In the Docking (Vina) filter, you can now specify a binding center by clicking on an atom in the viewer
  • Uploading a .sdf.gz no longer gives an error
  • You are now notified if you are over your limits before you submit a new screen job
  • You are now warned if you add the same property twice in the property filter
  • and various other fixes and improvements on the backend