I would like to try out the new KNIME workflows menu in Maestro. Where can I look at a few examples?

There are two places you can locate examples: in your default Schrödinger installation, and at the KNIME Workflows for Maestro web page.

To install one of the workflows from your default Schrödinger installation, go to Workflows → KNIME Workflows → Install examples → Cheminformatics → Nearest neighbor similarity distribution – install, for instance. Once this workflow is installed, you can run it from within Maestro by choosing Workflows → KNIME Workflows → Cheminformatics → Nearest neighbor distribution The nearest neighbor similarity distribution panel opens, indicating that the input this workflow requires is set to Selected entries – in the Project Table. Select several small molecule entries in your Project Table, and click the Run button in the Nearest Neighbor Distribution Similarity panel to launch the calculation. For this workflow, the results are returned in Maestro as a message in a pop-up panel. Another handy example in your default Schrödinger installation is General Tools → Process PDB codes, which prompts you for a PDB code list, and uses the codes in the list as input for preparing the PDB structures with the Protein Preparation Wizard.

To edit a KNIME workflow or some parameters in a workflows, click the Open in KNIME button to launch KNIME. Here, you can perform regular workflow manipulation in KNIME. Any changes you save in KNIME are automatically updated in your local copy of the workflow created during the installation step.

Workflow examples are also available at the new KNIME Workflows for Maestro web page (http://www.schrodinger.com/knimeworkflows/32/5/0/), which is periodically updated with new workflows. Here, you can download workflows you wish to install, and install them by going to Maestro → Workflows → KNIME workflows → Update.

One example workflow, available for download from the KNIME Workflows for Maestro page is Split and align multimers. Download and install this example. Then, import a multimeric protein such as PDB ID 1CX2 or 1SO2 into the Maestro Project Table. Navigate to Workflows → KNIME Workflows → General Tools → Split and align multimers and click the Run button in the Split and Align multimers panel. This particular workflow splits the selected Project Table entry into its component monomers, and performs a pairwise superposition of the C-alpha atoms in the binding site. Once the workflow completes, the results are returned as a new group in Maestro's Project Table. The title of the first node in this example is Selected entries which is why this particular workflow was run on the multimeric protein you imported into Maestro at the beginning of this exercise.

Additional information can be located in the Schrödinger Online Help, accessible from the Help menu in Maestro.

Keywords: KNIME-Maestro, coworker, colleague, share

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