Dear Reader,

We have just released Molegro Virtual Docker 5.0 with some very exciting new features. We have had several requests for a faster docking approach for large virtual screening runs, something which is now possible with our new GPU accelerated docking technique. We have also added Ligand Maps, which makes it possible to view compounds and their interactions in both 2D and 3D at the same time.

GPU Acceleration

It is now possible to perform virtual screening runs on a Graphics Processing Unit, a GPU, in Molegro Virtual Docker. The advantage of using a GPU is the speed - a modern GPU processor is able to deliver much more computational power than even the fastest CPU's.

We have created a special version of our molecular docking code, which can be executed on GPU's. With the appropriate hardware this makes it possible to dock a single compound in less than one second.

Our current implementation is built on the CUDA platform, which means that a Nvidia graphics card is required. Our implementation runs on standard Nvidia Geforce cards, so it is not necessary with dedicated Quadro or Tesla hardware. GPU acceleration is available on all our supported platforms: Windows, Linux, and Mac.

For more information, please see the Molegro Virtual Docker manual. Or, if you are interested in the technical aspects of GPU programming, we have published a paper on our first generation implementation: "GPU-accelerated high-accuracy molecular docking...". The version in MVD has been extended since this paper was released, but we will release a white paper with more details on the new version.

2D Ligand Maps

Since Ligand Maps integrates with the Ligand Energy Inspector, it is now easy to identify and visualize the interactions between the ligand and the protein receptor. And working in two dimensions makes it easier to select atoms and residues, and to get an overview of the interactions.

Other Changes

On Linux, our new builds now integrate better with the native graphics system - for instance, text is properly anti-aliased.

We also have a new installation procedure: per default, MVD now creates a working directory for log files and docking output in the user's home directory (for existing users, the old user settings will be used).

There are also several other minor tweaks and bug fixes in the new release, so if you haven't done it already, be sure to upgrade to the latest version of Molegro Virtual Docker (requires login).

Best regards,
Mikael Hvidtfeldt Christensen,
Head of Development,
Molegro.

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