Computational Chemistry

Nov

Neural Networks are interesting algorithms, but sometimes also a bit spooky. In this blog post I explore the possibilities for teaching the neural networks to generate completely novel drug like molecules. I have experimented for some time with recurrent neural networks with the LSTM architecture. In short, recurrent neural networks differ from more traditional feed forward neural networks because they do ...

Oct

Inspired by the success reported in my last blog post [Link] about the open source docking program rDock [http://rdock.sourceforge.net], I decided to investigate the docking accuracy performance of rDock more in depth. Once upon a time in the west the commercial docking program GOLD was benchmarked with two ...

Sep

Last time i tested the basics of the docking program rDock; Installation, basic setup and docking, as well as had a brief walkthrough about how to post-process the results with the rDock SD file utilities. However, as I've covered before, you should never use re-docking as an estimation of ...

Sep

rDock is an open source docking program, trying to solve the same kind of scientific questions as Autodock Vina, which I have covered in a couple of earlier blogposts. It was open sourced in 2012, but development of the earliest versions dates back to 1998. More details can be ...

May

In the two previous blog posts Ligand docking with Smina and Never use re-docking for ..., it was demonstrated how easy it is to dock a small ligand using Smina, and how deceptively accurate a docking program can be when using re-docking rather that cross-docking. It is however possible to re-tune the docking function to a specific purpose using machine ...

May

Re-docking of ligands found in PDB files are often used as a fast evaluation of a docking program before working with designed or other ligands. However this re-docking can give deceptively good results and it is recommended to instead test with cross docking. In this follow up blog post I give a short example of how it can be done. Cross ...

Apr

Moleculer Docking is a powerful technique for studying potential ligand-receptor interactions. It can be done with free tools. In this blog post I showcase the docking program Smina, a fork of Autodock Vina. Automated docking is the process of prediction of how one molecule binds to another in ...

Mar

Toxic compounds are most often something that we try to avoid when designing novel pharmaceutical compounds, so it could be nice to get a prediction if a compound is toxic even before ressources are used to synthesize it.  But what if it comes back as predicted ...

May

Molecular mechanics treats molecules as ball and spring systems using classical mechanical physics. Molecules are modeled as ”balls on springs”, and the total conformational energy are described as a sum of spring constants, torsional terms, vdWalls interaction, Couloumbic interactions etc. This collection of terms are known as a force field, and enables fast conformational ...