Autodock Vina

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 ...

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 ...