MCPairs v1.8 release is automatically available to all users:

MCPairs version 1.8 went live last weekend. All Online users are upgraded to the new platform, and all new tools are available to everyone. There is a small change in look and feel (the “Pizza Wheels” have been revamped, for example) but just about everything is in the same place. The big new feature is automatic R-Group decomposition and analysis tables. This can export fully editable Powerpoint presentations. There are useful new features, like the ability to paste in a structure from multiple drawing tools. For the computational chemists there is beta-release of SARkush(R) – a brand new analysis tool – send in a file of compounds and primary potency, and it will automatically generate Markush structures for SAR understanding and R-Group spreadsheets.

Drop us an email at for an ‘update’ session.

Automatic R-Group Table and Export to Powerpoint

The big brand new feature for v1.8 is the generation of RGroup tables for SAR analysis and preparation of presentation slides. This is found under the ‘Compound-to-Pairs tool’. The manual copying of data from a database to a table in slide presentation is a laborious process and prone to human error. On top that, all the structures need to be drawn with all the R-Groups aligned. While we may want to take our time for a conference presentation, the bulk of our communications are internal. Here we can make huge time savings if we could just rapidly generate tables of data to communicate the key messages so teams can make decisions. The faster we can generate these, the more time there is to absorb the SAR, think about the implications, and create new designs.

Here is a screen shot of an R Group view with a populated set of compounds:

RGroup view v1 8

So you can see what is looks like in MCPairs – here is a movie of the workflow to R-Group tables:


Paste Structures from ClipBoard – Use your own drawing package

RuleDesign(R), SpotDesign(R), Toxophores and Pharmacophore all have the same drawing package as one of the methods to input a structure for analysis.  We have added a new feature to ‘paste’ the structure from a drawing package. So you can grab you structure from ChemDraw (for example) as a Mol3000 object and click the little blue button to drop the structure in.  The method of copy to clipboard is slightly different depending on the drawing package you use.

mcpairs 1 8 paste from clipboard

Click the Blue button to paste from ClipBoard

New look Pizza Wheels

We have re-written the module that generates the “Pizza Wheels”, where we summarise the pair data for a Broad set of Goals. This gives us better control and support for the future.  In essence they are the same, but we increased the contrast on hover-over, so the numbers stand out. As before, clicking on a wedge gives access to the pair data. Which leads us nicely onto the new Pair View Plot.

pizza wheel new style v1 8

Drilling down to single matched Pairs and The Pair View Plots

Whichever way you get to the Rule-to-Pairs viewer, from a hyperlink or clicking a slice of Pizza in the wheel, there are two new features to look for. On the right the list of Endpoints (Assays) with matched pairs of the given transformation now drills down to single matched pair; this provides much more depth than previous versions and so there is a greater chance of finding potency data relevant to your target. The example below shows single matched pairs for an epigenetic target and some integrins.

Drill down to single pairs

Endpoints drill down to 1pair

Once you have some pairs in the table we can click on the Pair View Plot


…and the Pair View Plot appears in a lightbox. Hover over the dots to see each matched pair on the right. The units reflect those shown in the table and can be linear (log scale) or non-linear units.

Pair plotsMCPairsc1 8

As we have done here, you can take a partial screen shot OR click the Export Plot to download an image that can be inserted into your slide presentation.


SARkush(R) – A beta release for Computational Chemists

This is our first release of SARkush(R) for computational chemists to explore – an update to the latest version of the command line tool (mcpcli) will be required.  Sending in a file of compounds and data to the ‘sarkush’ options runs a process in the ‘MyPairs’ suite of tools to automatically generate ‘Markush’ like structures. Multiple series of compounds can be submitted without the need to create or maintain a list of ‘Core’ descriptors. The output is a zip file of goodies. The primary file is a summary of the different series and SARkush generated (as shown below).

Here is an example for a small file of EGFR inhibitors:

SARkush summary output V1 8

There is a separate file of the compounds ‘under’ each SARkush with an R-Group table (example below is SARkush 1 from above).

Here is Series 1 from the above file.

Rgroup tabel from SARkush v1 8

There we go – as a reminder:

Drop us an email at for an ‘update’ session.