Blog

The Blog is a collection of News, Blog posts, technical tips and tricks and other writings from my sphere of interest.
- Esben Jannik Bjerrum

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

I had the pleasure and opportunity to pitch for 5 minutes at the first Meet and Greet meeting at COBIS. Its an new, regular internal event for all the companies there, where we meet and network over a cup of coffee and a croissant. I was lucky to be one of the three that got the permission to pitch and ...

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

Pay it forward

I have volunteered as a Mentor in the Mentor-Mentee network arranged by PharmaDanmark. The idea is to match up young professionals with more experienced seniors for professional sparring and discussion focusing on promoting the Mentees career. Pharmadanmark provided an extensive guide for a successful meetings and  including many suggestions and practical tools ...

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

RDKit UGM 2016

I'm looking forward for the first to attend the RDKit user group meeting from 26-28 October 2016 in Basel, Switzerland. RDKit is an open source chemoinformatics toolkit written in c++ with python bindings and extensions. Additionally, it has a database cartridge, which makes it quite useful for handling chemical information and storage ...

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 ...

Aug

During the summer holidays I gave a presentation with the title "Open Drug Discovery" at the Gifted Children summer camp 2016. The presentation covered drug discovery and open innovation in drug discovery research, with a focus on what possibilities amateurs have to contribute. Gifted Children is an association for gifted children and their parents. Gifted children advocates a better understanding and ...

Jun

Sometimes it comes in handy to be able to note a date or time quickly in Excel. This happens often when using Excel sheets for logging purposes and registration of laboratory experiments and results. This post illustrates how to make a drop-down with todays date where the entered date will not update automatically. Data validation for drop-down menus For this purpose the ...

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 ...

Apr

When I have been working with chemical databases and import of molecules I have encountered numerous problems with the way chemical structures are drawn. Most often the problem arises as creative users in the past have had a problem with registering a compound the way they wanted it. Sometimes the used ...

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 ...