Schrödinger KNIME Extensions allow scientists to protoype, validate, automate, and deploy multi-step workflows. In this installment of KNIME Questions and Answers, Schrödinger’s KNIME Extensions Associate Product Manager Jean-Christophe Mozziconacci talks about how to install workflows that can be run directly from Maestro without opening the KNIME GUI, how to exchange structures between KNIME and Maestro, and more.
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Q. I regularly create KNIME workflows for other chemists in my group who are less familiar with KNIME. Is there a straightforward way they can run my workflows?
A. With the latest release of Schrödinger Suite 2012, your coworkers can now run KNIME workflows directly from the Maestro interface without having to be familiar with KNIME: the workflows are run behind the scenes without opening the KNIME graphical interface. To create workflows that your coworkers can run from Maestro, go to the Workflows menu in Maestro, and select KNIME Workflows → New. In KNIME, create your workflow, or import an existing one. Then, edit the Reader, Writer, and Quick Form node names to specify for inputs and outputs of the workflow, and the parameters to expose in the Maestro start-up panel. For details, go to Help → Online Help in Maestro, and search for the article titled “Editing KNIME Workflows for Use Within Maestro”.
To try some example KNIME Workflows for Maestro, see this Knowledge Base article.
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Q. I tried out the Run Maestro 1:1 metanode and I find it useful for performing interactive steps in a workflow. However, I’d like to keep the Maestro session open and exchange structures with KNIME. Is there any way to do this?
A. There is a new Structure Exchange with KNIME mode in Maestro in Suite 2012 so that you can now do exactly this. Simply launch Maestro and start the dedicated server under Workflows → Establish Structure Exchange with KNIME. Launch KNIME and include the new KNIME-Maestro Connector Node in your workflow. A good example usage of the KNIME-Maestro Connector node is in the Validate docking parameters with KNIME workflow, available for download from our KNIME Workflows page.
When this KNIME-Maestro Connector node is executed, the input structures to the node are added to the Maestro Project Table. If the node does not take an input, it will appear in the list of KNIME nodes connected in the Maestro Structure Exchange with KNIME panel, and you can then pass structures from Maestro to this KNIME node.
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Q. I’d like to launch PyMOL to visualize results after running a couple of my KNIME workflows. How can I do this?
A. You can use a metanode titled Run PyMOL. This metanode is used in the "Run PyMOL" workflow example, shown below. Explore this workflow to see how you can launch PyMOL to visualize a file of ligands, and/or run PyMOL commands (save a ray-traced image and the associated PyMOL session) and pass the output to the downstream node.
Figure 1: At left, the examples included in the Run PyMOL workflow are shown. At right, the Run PyMOL metanode configuration panel is shown.
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Q. I’d like to create a KNIME workflow that searches for binding sites and docks a library of ligands at those sites. How can I do this with KNIME?
A. We have posted a new example workflow for binding site identification and ligand docking, titled “SiteMap and Glide grid generation.” In this workflow shown below, a set of PDB structures is prepared, and possible binding sites are identified using SiteMap. Since there is not a SiteMap node available at this time, SiteMap is run with a Python script node contained in a metanode, and the settings for the metanode are specified by upstream Quickform nodes. The identified possible sites and the corresponding site surfaces are stored and can be inspected in Maestro. The Python script also includes commands that generate a Glide grid for each of the identified sites; these grids are written to disk for future use in docking ligands.
Figure 2: The SiteMap and Glide grid generation workflow example.
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Q. I don’t have a license for the Schrödinger extensions. Can I still read and write Maestro files, and start Maestro from KNIME?
A. Yes, you can still read and write Maestro files, and start Maestro from KNIME. You do not need a Schrödinger KNIME license to run the nodes for reading, converting, and writing files, or for running the nodes for executing Maestro and Canvas from the KNIME interface. You can also execute the new KNIME-Maestro Connector node without a license, so the new KNIME menus in Maestro (described above) are also available to you.
Additionally, the Python script nodes that enable you to run scripts and use our APIs now don’t require a KNIME license (see the "Python Script Node Use-cases" workflow and the other workflows listed within the Python Script Node Use-cases example). You can also use other C-based APIs included in the path (see www.schrodinger.com/kb/1072 for details).
All of these nodes are available in KNIME with your Schrödinger installation, or you can add these nodes to a stand-alone installation using our update site. For detailed instructions on obtaining and installing the latest KNIME extensions, see this Knowledge Base article.
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