Batch Maestro Jobs in KNIME

[richards99]

Is there any plans to be able to do a lot of the Jaguar-Maestro functions within a KNIME workflow.

For instance I would like to be able to get pKa calculations on a specific proton in 10 different analogues using the lowest energy conformer.

Doing this in Maestro seems tricky as I'm unable to set the batch of 10 calculating overnight without them terminating. Can it be possible to highlight the desired proton in a chemical sketcher in KNIME, use the LigPrep/ConfGen tools to get the lowest energy conformer and then another node to calculate the pKa of the highlighted proton. This would be a good user friendly way of doing batch pKa predictions.

If this became possible, it would be useful to apply the same logic to calculating the partial charge on selected atoms, as well as predicted NMR chemical shifts too.

On top of that, nodes to generate electron density mappings, and dipole moments of the whole molecule would be useful too.

Chemists generally struggle with the learning curve of Maestro and therefore it would bring the accessibility of these tools closer to the medicinal chemist via KNIME. 

Thanks

Simon.

[jcmozzic]

Dear Simon,

 

We don't have a Jaguar pKa node for now but it should be pretty easy to alter the jaguarCLI.py script to run such a calculation. I would suggest we discuss the details offline (please send an email to help@schrodinger.com).

The ESP charges can be calculated with the Jaguar minimization or single point nodes and then extracted with the MAE parser node.

On our workflow page (http://www.schrodinger.com/knimeworkflows/) you can find an example using these nodes that might be of interest to you.

We have also an NMR shielding constants node and I'm going to add a workflow example to the page. I have a workflow that calculates and displays the electron density surface I could also provide to you.

Best regards,

 

Jean-Christophe

 

Senior Applications Scientist and KNIME Associate Product Manager, Schrödinger