Blog

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 ...

Mar

In the NIR news (again)…..

Esben Jannik Bjerrum is in the (NIR) News again. This second part concludes the announcement of the Fulgur application, by introducing an overview of the source code as well as highlighting a way of working with Matlab GUI programming that takes the synchronization hassles out of it. The first part of the articles introduced the Fulgur program itself, which is ...

Feb

The chemoinformatics package Rdkit has is strength with handling small organic molecules. These molecules are characterized by a large diversity in chemical structures. A description of the exact way the atoms bond together are necessary to understand what molecule it is. Biological macro molecules are often build from repeating sequences of standard building blocks, such as amino-acids or ...

Feb

Feature selection is a powerful way of reducing the complexity of a machine learning or statistical model. But feature selection must be done in the right way, or you may end up cheating yourself or others. Later we will also see if green jelly beans are truly associated with acne. When working with machine learning, it may be a good idea ...