The Schrödinger KNIME extensions

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1 The Schrödinger KNIME extensions Computational Chemistry and Cheminformatics in a workflow environment Jean-Christophe Mozziconacci Volker Eyrich KNIME UGM, Zurich, February 2014

2 The Schrödinger extensions Computational chemistry and drug design 150+ nodes Linux, Mac, Windows 32 and 64 bit Molecular Mechanics Macromodel Molecular Dynamics Desmond Quantum Mechanics Jaguar Cheminformatics Canvas Pharmacophore modeling Phase Combinatorial Libraries Combiglide Docking Glide Protein Structure Prediction Prime, IFD Maestro integration - Workflow execution - Structure exchange Set of free nodes (see KB:1710) Protein preparation Ligand preparation LigPrep, Epik Property generation Qikprop... Filtering Data and structure manipulation Scripting shell, Python Reporting Run Maestro, PyMOL New features in 2013 and Suite will be released this week: Includes the latest version of KNIME (v2.9)

3 Parameter flow variables for more nodes Use any command line option not exposed in the node configuration panel Glide Ligand Docking Can use any Glide Simple Input file option eg Core constraints: GlideLigandDocking-ref_ligand_file = <path/file.mae> GlideLigandDocking-use_ref_ligand = yes glide_sif.py... -ref_ligand_file /tmp/ref.mae -use_ref_ligand yes Prime Build Homology Modelling - use a specific template

4 Simpler Batch Execution Command line to be run generated based on node annotations KNIME in batch wrapper list the allowed nodes and corresponding tags $SCHRODINGER/run -FROM maestro KNIME_batch.py <workflow.zip workspace/workflow> -printallowed Text Node Action Structure file Molecule Reader Read the first file specified in the node. Selected entries Molecule Reader Read the entries that are selected in the Project Table. (Maestro only)... Text file CSV Writer Write the output to specified file. GUIsetting Double Input, Add a text box control to the panel Integer Input, and assign the value that is set in String Input the text box. -printusage, -printcmd, -run, -GUI options (already in Suite ) $SCHRODINGER/run -FROM maestro KNIME_batch.py Shape screening.zip -run -imae /tmp/fragments.mae -imae1 /tmp/query.mae -omae /tmp/phaseshape.mae See Shape screening workflow example:

5 Run workflows from Maestro (since Suite 2012)

6 Webservice Can invoke web service to execute LigPrep node schrodinger.hosts: name: my_server host: my_machine.schrodinger.com port: 8080 processors: 3 Execute some Schrödinger backends through the Generic Web Service Client node with 1 input and 1 output eg LigPrep, QikProp... See General tools > Webservice workflow example

7 Run PyMOL and Glide grid writer Run PyMOL Structures ungrouped to operate more easily on the structures New Glide grid writer node Glide Grid Generation - Save options Glide Multiple Grid Reader -... Columns indicating original file location

8 KNIME workflow page Cheminformatics Substructure Search Clustering, diversity selection, similarity search Database analysis, MCS Docking and post-processing Binding site (SiteMap, grid generation) Docking, Virtual screening, Ensemble docking Loop over docking parameters Validate docking parameters using the Maestro connector node Pharmacophore modeling Shape screening, hypothesis identification, database screening Molecular Mechanics Compare conformational search methods Conformational search and post-processing Quantum mechanics ESP charges, Jaguar pka, QM properties, Semiempirical Conformational search and QM refinement (using the Report designer) Molecular Dynamics: Desmond simulation Library design: Library enumeration Homology modeling Model building and refinement Induced Fit Docking Real World Examples Vendor database preparation SiteMap and docking Binding site shape clustering Labs: Run Maestro 1:1, Glide grid writer, Parameter flow variables General tools Split and align multimers Python script, Chemistry external tool, Run maestro command node use-cases Run PyMOL Workflows in the current workspace KNIME desktop GroupBy, loop examples

9 Workshop on Friday Applications of the Parameter flow variables Chemistry external tool node examples Simpler batch execution Applications of some recent new features ftp://ftp.schrodinger.com/support/hidden/jcmozzic/zurichugm.zip ZurichUGMnoData.zip

10 Schrodinger KNIME extensions Jean-Christophe KNIME extensions Product Manager Mozziconacci Volker Eyrich Vice President of Technology Ravikiran Kuppuraj Main developer Matt Wirtala QA Daniel Schafer, Technical support Jeff Saunders and Pavel Golubkov Jarred Yacob Marketing Schrödinger Developers

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