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    • Esben Jannik Bjerrum
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    • Esben Jannik Bjerrum

Teaching Computers Molecular Creativity

Esben Jannik Bjerrum/ November 7, 2016

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

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Wildcard scoring function beaten by rDock!

Esben Jannik Bjerrum/ October 1, 2016

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

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Cross docking test with rDock

Esben Jannik Bjerrum/ September 13, 2016

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

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Test drivin' rDock

Esben Jannik Bjerrum/ September 5, 2016

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

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Machine Learning optimization of Smina cross docking accuracy

Esben Jannik Bjerrum/ May 19, 2016

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

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Never use re-docking for estimation of docking accuracy

Esben Jannik Bjerrum/ May 11, 2016

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

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Ligand docking with Smina

Esben Jannik Bjerrum/ April 28, 2016

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

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Learn how to map a simple Ames mutagenicity model to molecular features using RDkit.

Esben Jannik Bjerrum/ March 31, 2016

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

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Scripting Molecular Mechanics Calculations using Tinker and sdf2xyz2sdf

Esben Jannik Bjerrum/ May 11, 2015

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

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