Macs in Chemistry

Insanely Great Science

mmpdb: An Open Source Matched Molecular Pair Platform for Large Multi-Property Datasets


An interesting paper on chemrxiv DOI

Matched Molecular Pair Analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property datasets. Here we present mmpdb, an open source Matched Molecular Pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large datasets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from


NMR solvent peaks


I just noticed this mentioned on Twitter and so I've added it to the Mobile Science site.

NMR Solvent peaks is a conveniently-searchable version of the ungainly table of NMR data most organic chemists keep a copy of nearby. Instead of searching through the table for a peak near your unidentified peak, just enter your solvent and the peak's multiplicity and location and you'll have a short list of candidate impurities

There is also a web-based version and a twitter feed for submitting bugs and finding out about updates.

There are a number of other NMR apps available


WWDC 2018


The Apple Worldwide Developers Conference takes place in San Jose, CA, June 4–8. The opportunity to buy tickets to WWDC18 is offered by random selection. Registration is open until Thursday, March 22, 2018 at 10:00 a.m. PDT

To register, you must be a member of the Apple Developer Program or Apple Developer Enterprise Program as of March 13, 2018 at 10:00 a.m. PDT, and agree to the WWDC18 Registration and Attendance Policy. Your membership must be current, valid, and in good standing from this date until the end of WWDC18.


Flagging Potential Kinase Inhibitors


Most of kinase inhibitors bind in the region of the ATP binding site using the hydrogen bonding interactions of the hinge region shown in the schematic below. We can use the knowledge of these hinge binding motifs to flag potential kinase inhibitors.




BBEdit 12.1.2 Released


BBEdit 12.1.2 is a minor update to my favourite text editor.

From the release notes.

There's a new item in the Application preferences, as part of the software update settings: "Early Access". You can use this to turn on (or off) notification of pre-release maintenance updates for the version of BBEdit that you're using. (Note that even if you turn on Early Access, you will not receive notice of pre-release versions of feature updates or major upgrades.)

A new setting in the "Editing" preferences allows you to control whether tick marks appear in the scroll bar for Live Search matches. Turning this off can be useful if you're working in very large files and have so many results that the application stalls while trying to update the marks.

There are also a number of bug fixes including.

Fixed bug in which the Markdown tokenizer was confused by empty URL references (e.g. ) in such a way that editing in certain subsequent parts of the file would cause syntax coloring to get out of whack. This change also fixes a bug in the Markdown syntax coloring in which links with an empty description or URL were not properly recognized and colored.

BBEdit 12.1.2 requires Mac OS X 10.11.6 or later, and is compatible with macOS 10.13 "High Sierra"

I use BBEdit extensively for Markdown editing but there are a number of alternatives.