Blog

Feb

New option to follow comments

A new Wordpress plugin has been installed, which enables commenters to get notified when additional comments or replys are added to the blog posts. This did only work before for registered users of the Wordpress, such as writers and admins. This was rather unfortunate. But now it is not necessary to ...

Jan

I found some interesting toxicology datasets from the Tox21 challenge, and wanted to see if it was possible to build a toxicology predictor using a deep neural network. I don't know how many layers a neural network actually has to have to be called "deep", but its a buzz word, so ...

Jan

In the last blogpost the battle tested principal components analysis (PCA) was used as a dimensionality reduction tool. This time we'll take a deeper look into chemical space by using a deep learning neural autoencoder, by testing some of the newer tools based on neural networks which has shown promising results. ...

Dec

As covered before, chemical space is huge. So it could be nice if this multidimensional molecular space could be reduced and visualized to get an idea about where how query molecules relate to one another. This small tutorial show a simple example of how this could be done with the PCA decomposition from scikit-learn and molecular fingerprints calculated with ...

Dec

Neural networks are interesting models underlying much of the newest AI applications and algorithms. Recent advances in training algorithms and GPU enabled code together with publicly available highly efficient libraries such as Google's Tensorflow or Theano makes them highly interesting for modelling molecular data. Here I explore the high level Neural Network ...

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 ...

Nov

BioAgora 2016

Wildcard Pharmaceutical Consulting was represented at the Bioagora2016 at Frederiksberg Campus centered about biomarkers. Read more about the event at bioagora.dk

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 ...