Wednesday, May 30, 2012

New release! Live-docking, property filtering, new table view

After the first release of mcule, which included basic searching functionalities, we have been working hard on the integration of several new features. I'm pleased to introduce:

Docking (Vina)

Yes! Docking is part of the release pack, and we believe that this will really make a difference! There are a few docking servers available on the net, but have you ever heard about live-docking? Check this out:

After you launched the docking you can start browsing the results as soon as the first few calculations are finished.
One other cool functionality is that you can select your target from among ~10k PDB structures prepared for docking. Many thanks for the group of Prof. Didier Rognan for allowing the integration of sc-PDB [Meslamani J, Rognan D, Kellenberger E. sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins. Bioinformatics. 2011 May 1;27(9):1324-6.] with mcule. This is a great benefit for our users as you can now directly select targets by searching for PDB ID, Protein name, Organism name, UniProt Name/Accession ID/Taxonomic ID. The centre of the binding site will be also automatically determined based on the position of the co-crystallized ligand. All these protein structures have been automatically prepared for docking. Besides selecting your macromolecule from the sc-PDB database, you can upload your own structures as well.
For docking, we use the latest version of the open-source docking tool AutoDock Vina [Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010 Jan 30;31(2):455-61.]. We were quite satisfied with Vina in the past, as it was involved in our GPCR fragment library design protocol, which yielded 100% hit rate. 


There is a property filter, where you can set minimum and maximum boundaries. Available properties are either calculated from the InChI string (molar mass, number of atoms, heavy atoms, hydrogens, heteroatoms, stereocentres, cis-trans double bonds), or by OpenBabel (logP, PSA, molar refractivity, number of rings, rotatable bonds, H-bond donors, H-bond acceptors) [O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011 Oct 7;3:33.]. Besides these, rule-of-five and rule-of-three violations are also calculated.

Table View

We have designed a new view, which makes browsing the results even more efficient.

In the new table view you can set which properties (including screening results, e.g. docking scores) you would like to display. Now, you might have seen molecule databases displayed in a useful and transparent way on the web before (there are not many good examples though), but I doubt you have ever been able to sort that database as blindingly fast as you can from now at mcule.com. Believe it or not, sorting of many hundreds of thousands or even millions of molecules can be done in a few seconds(!). Remember that you are using a website and not a desktop application.


There is another filter, called Sampler. It can be used to cut the database at a certain threshold and retain only the top x number of molecules. By default it retains the top molecules highest ranked by the previous filter, but it can be set to sample the molecule collection randomly.

It is also important to mention that more advanced features are provided for free with some limitations. The maximum number of molecules for docking is currently set to 500 per month. Sampler is an efficient way to reduce the number of input molecules for such limited filters. We will provide subscriptions with much less boundaries on the website soon. Until then, contact us if you need more!

OK. So now you can go and do some docking if you like, but remember that many other features are underway, so there is more to come! Keep looking at this blog for more!


  1. Great job for publishing such a beneficial web site. Your web log isn’t only useful but it is additionally really creative too. There tend to be not many people who can certainly write not so simple posts that artistically. Continue the nice writing Ohio Car Insurance

  2. The information you have posted is very useful. The sites you have referred was good. Thanks for sharing... Bukit 828 Freehold Condo Bukit Panjang MRT Station

  3. Great article with excellent idea!Thank you for such a valuable article. I really appreciate for this great information.. The Hyde Orchard

  4. Thank you for taking the time to publish this information very useful! Mayfair Modern Beauty World

  5. Pretty good post. I just stumbled upon your blog and wanted to say that I have really enjoyed reading your blog posts. Any way I'll be subscribing to your feed and I hope you post again soon. Big thanks for the useful info. compare auto insurance rates

  6. Find top realtors in your city or town that go the extra mile and advertise in all the top spots. Our Real Estate Brokers use an inside platform to connect buyers and sellers through Agents in our system. We have lists of developers, builders. And do lan assembly packages to get the best value for your home or property. When only the finest Realtor will do to work with your most valuable asset then look no further than our hand picked Real Estate Brokers list. If you want more info click here link : Real Estate Brokers

  7. This comment has been removed by the author.

  8. It proved to be Very helpful to me and I am sure to all the commentators here! villa for sale Los Flamingos