MCPairs v1.9 release is automatically available to all users:

MCPairs version 1.9 went live last weekend. All Online users are upgraded to the new platform, and all new tools are available to everyone. On logging on you will notice the change in the layout of the dashboard as CoreDesign® has been added. This joins RuleDesign® and SpotDesign® as our “triumvirate” of design tools. As the name suggests CoreDesign® makes changes to Rings and Linkers (Rinkers) in molecules, so can be considered a scaffold hoping tool. If you would like an ‘update’ training session drop us a line. For the adventurous, a quick tour of the feature is below – get stuck in!  As requested, SDF file output is now available for our Design tools – compounds are automatically aligned where possible.

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

The New Dashboard

MCPairsv1 9 Design Dashboard

Where is Compound-To-Pairs?

This has moved down slightly, into a new section called ‘Data Explorers’.

MCPairs v1 9 Dex Dashboard

A quick tour of CoreDesign®

The big brand new feature for v1.9 is CoreDesign®. Data entry is similar to RuleDesign®, so should be straight forward for people to use. A key difference is the need to define ‘the core’ – the part of the molecule you want good scaffold hop ideas. After highlighting part of the molecule, the Submit button will turn Green. In our example below, the hinge binding heterocycle has been selected by clicking the highlight tool (blue circle), and clicking all the atoms of the heterocycle. Press Submit.

Here is a screen shot of input window of CoreDesign®

MCPairs v1 9 CoreDesign Input

Paste Structures from ClipBoard – Use your own drawing package

CoreDesign®, RuleDesign®, SpotDesign®, Toxophores and Pharmacophore all have the same drawing package as one of the methods to enter a structure for analysis.  We added a feature v1.8 to ‘paste’ the structure from a drawing package. So you can grab your structure from ChemDraw (for example) as a Mol3000 object and click the little blue button to drop the structure in.  The method of copying 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

Looking at CoreDesign® results:

The lightest view is to explore the results in the browser. They can be exported to file and opened in other tools for further filtering and processing. In the browser we recommend sorting by Relative Molecular Mass (RMM), so we start looking at the smallest molecule and moving to the largest.

MCPairs v1 9 CoreDesign results RMM

As with RuleDesign compounds can be selected and a subset exported.  Try clicking the View and Explore buttons.

Clicking View button shows further details on the matched pair data:

MCPairs v1 9 CoreDesign Pair counts

…and there are links to the literature and patents. These are the matched pairs where the chemical transformation, leading to the ring or linker change, has been observed.

MCPairs v1 9 CoreDesign literature

How does CoreDesign® work?

The easiest way to find out is to watch Dr Jessica Stacey talk at the RDkit forum (it takes a few moments before the presentation starts – apologies, we were not in charge of the editing!)

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