Tethered minimization of small molecules with RDKit

Tethered minimization of small molecules with RDKit

I think that’s my first RDKit post! So reason to celebrate!

Here' I’ll focus on a very nice feature available in Open Source Software and very useful in daily structure based but even ligand based drug design tasks.

The problem

How can I dock small molecules into a receptor and avoid as much as possible the “what is the right pose” problem?

We're starting a Slack community for our customers! Here's why.

We're starting a Slack community for our customers! Here's why.

Slack  is a really cool real-time team messaging app. The conversations can be held in both open and closed groups as well as in one-to-one discussions. We've been using it internally for over a year now. It quickly became extremely popular, to the point of reaching more than 300K messages in less than a year (with 35 users per week on average). And now we are opening it to you !

Enabling Matched Molecular Pairs Analysis for Target Activity Prediction on Small Datasets

With the very fresh 2.0 release of the Discngine Chemistry Collection for Pipeline Pilot nifty new functionality is available to Pipeline Pilot users. Find out more about the new release of the Chemistry Collection.

This post describes one of these new features, fuzzy context specific matched molecular pairs (fcsMMPs), why you should adopt them and a few examples of what you can do with this. Note that this post focuses on target activity prediction (fairly unsual for MMP analysis), but everything that is described here applies to more classical property prediction too.

Everything that is shown here can be done with this Pipeline Pilot Component Collection. Even the data is included. 

If you do not feel 100% familiar with the concepts behind matched molecular pairs analysis, please read through the introductory part below. If you know what a transformation, a common core and a context is and have done matched pairs effect analysis in the past, you can directly go to the fcsMMP specific part of this post