I love MOE, it’s a great piece of software, but unfortunately it’s not free and now that I’m nor in academia, nor in a pharma company I find myself unable to further develop an approach I implemented in the past which is kind of frustrating to put it politely. The same goes for Amber.
So I started to look for alternatives, also under a gentle demand from Anthony (poking me regularly) who wanted to apply the whole approach in his fragment screening pipeline. That’s in the scope of the crazy impressive XChem project. If you haven’t heard / read about that check it out - it gives you a bit of an insight on what will be possible very near future in xray crystallography!

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?

A brief walkthrough on how to compile the molfile plugin for VMD in order to use it for programming and integrating into your own code.

In this blogpost we will present our latest developments to handle more efficiently large MMP datasets and databases, how to keep them up to date and how to develop responsive applications on top of that. 

If you ever had to manage, administer or install a Pipeline Pilot server you know that this is usually not a piece of cake. It's a fairly long process, involves a lot of more or less manual steps (that you could automate, but did you do it so far?)

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. 

F1000Prime Associate Faculty Membership : Good or Bad ?

PBS is widely used as queuing system on small size to huge clusters. This is just a little post to resume somehow all installation steps necessary to get a single node torque server running on Centos 6.4 (64bit).

Dassault Systèmes acquires Accelrys!