Getting Started with the NeuroDeRisk Toolbox

The best way to get started are the ready-to-use workflows that are already included in the toolbox installation. This page guides you through your first execution of one of these workflows.

Info

If you installed KNIME and the toolbox extensions separately, you can also manually download the example workflows and import them into your KNIME installation, as described in the KNIME Usage section of this documentation.

Setup

Start by loading a ready-to-use workflow. In the KNIME Explorer panel in the top left of the user interface, double-click the IL-Profiling workflow:

If this is the first time you are using the toolbox, a pop-up will be shown, asking for license activation:

Clicking the Activate button will trigger another dialog, asking for your License serial number. If you are eligible to use the toolbox, you should have received a serial number. Otherwise, please get in contact with Inte:Ligand.

After activating the license, there is one final step to do before you can start configuring the profiling workflow for the first time. Open the Configure dialog of the NeuroDeRisk IL Profiler and connect to the Inte:Ligand servers. To do this, you need a set of credentials:

After connecting, click OK to close the Configure dialog. To get started, we will use the default settings.

Info

License activation and authentication in the profiler node have to be done only once. Your license and credentials will be saved for future use.

Running the Workflow

After activating the license and passing authentication in the, we have to provide input structures that should be screened against the 3D-neurotoxicophore models that are provided by the NeuroDeRisk IL Profiler. The NeuroDeRisk Toolbox provides several ways to input molecules, that are described in detail in a separate documentation section section. For the purpose of this guide, we will use the Molecule 2D Editor Node. Right-click this node and click Configure:

Then, draw an arbitrary 2D molecule structure. The profiler will take care of generating 3D conformations and further preparing the molecule for screening. Once you are finished drawing, click the OK button located in the bottom of the Molecule 2D Editor's dialog.

Then, you are ready to execute the workflows. Right-click the output node and click Execute:

Congratulations, you have run your first NeuroDeRisk profiling experiment! The results of the profiler node can be analyzed via right-click->Output molecule table, and right-click->View:heat map. This is described along with options to save the results in the NeuroDeRisk IL Profiler section.

Next Steps

For more advanced usage of the toolbox, please refer to the next section of this documentation, which gives a more general overview of the KNIME platform. The documentation further contains sections for specific use cases, such as chemical structure profiling and drug selection/MoA analysis.

Question

Do you have any feedback regarding this documentation or the toolbox? Don't hesitate to get in contact with Inte:Ligand.