MolSync reaction searching: basic pieces in place

molsync_rxnsrch1The last update of the MolSync site added a visual overhaul and molecule searching. Today’s update brings along the basic UI for reaction searching, and preliminary functionality for various kinds of reaction searching by structure.

The reaction searching interface looks a lot like the molecule searching interface. The main difference is that instead of one rectangular box for sketching a structure, there are two of them, connected by an arrow. This should tip off most chemists to the idea that it’s a transformation that is being described. The other difference is that the 3 types of searches are called Component, Transform and Similarity. And the randomly presented bundle-of-things that is shown on loading is made up of reactions, rather than molecules.

To do interesting reaction searching, one must first give it something to search for, one way being to use the rather new web-based sketcher:


Once the requisite query or queries have been provided, hitting the search button will hopefully bring up something interesting:


In this case, the request indicates that we would like a benzyl alcohol to aldehyde conversion, which is found with the first result. Now, this would be the time to point out that the full sophistication of reaction search types hasn’t been connected up yet. The underlying technology on the back-end is ready to go with regard to searching for specific types of transforms, but the UI does not yet have a way for users to specify atom-to-atom mapping. Once that is done, the workflow will allow the queries to be defined very specifically, to capture the actual chemistry going on, rather than a relatively unconstrained substructure search. Also, at the time of writing, the similarity search type isn’t implemented. This will make use of a variation on the ECFP6/Tanimoto similarity metric, adapted to make use of atom mapping/transform information.

There are quite a few ways to compose a reaction search using one-or-more structures, and the help page makes an attempt to explain it concisely (without going into too much detail):


The current implementation should be considered to be a preview, but watch for more functionality to come together rapidly.


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