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KNIME Workflows

KNIME Workflows for Schrödinger Suite 2009 can be downloaded from this page.

Below are many useful workflows for performing automation, customization, and scientific augmentation to the Schrödinger Suite. The workflows additionally provide a framework for scientists to create custom workflows. Check back regularly, as improvements to existing workflows and new workflows are added frequently. Send requests for improvements or new workflows to help@schrodinger.com.

Note: You can view the list of available workflows without logging in, but you must log in to download the workflows. If you are not already logged in to the site, your selection will be saved and you will be prompted to log in before the download will begin. If you do not already have a logon account, please click here to request one.



Select Workflows

Listed below are example KNIME Workflows that utilize many of the Schrödinger KNIME Extensions (Nodes) as well as many other built-in tools.


Check the boxes next to the workflows you wish to download, read the Important Notes, then proceed below to check the Important Notes checkbox and click the Download button.
Note: If you are not already logged in to the site, your selection will be saved and you will be prompted to log in. If you do not already have a logon account, please click here to request one.

Select Description Updated
Cheminformatics
Cluster by Fingerprint: Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of clusters based on the Kelley penalty. Select diverse representatives per cluster. [Revision: 1 #1.1, 1-2 #1.1, 1-3 #2.2, 1-4 #2.5] [Requires: Canvas]

[List of nodes: File Reader, Column Filter, MAE_to_Smiles, Group MAE, Chemistry External Tool 0_1, TableRow To Variable, Text Viewer, Generate Pairwise Matrix, Dissimilarity Selection _from Matrix_, Row Iterator Loop Start, Loop End, Extract MAE Properties, Lookup and Add Columns, Fingerprint Generation, Ungroup MAE, Row Filter, Rename, Concatenate, Inject Variables _Data_, Build Report for Clustering _from Matrix_, Sorter, Column Resorter, Hierarchical Clustering _from Matrix_, Molecule_to_MAE, GroupBy]

   11/02/2009
Database Analysis: Assess the coverage of a database from the distribution of the distance to the nearest neighbor of each molecule in the database. List the three most similar compounds for each compound in the database. [Revision: 1 #2.1, 1-2 #2.1] [Requires: Canvas]

[List of nodes: Text Viewer, GroupBy, Generate Pairwise Matrix, Numeric Binner, Molecule Reader, Math Formula, Transpose, RowID, Column Filter, Java Snippet, Row Filter, Sorter, Inject Variables _Data_, Row Iterator Loop Start, Loop End, Create Collection Column, Joiner, Histogram Chart, Convert Matrix to Table, Fingerprint Generation, Similarity Matrix _from Molecules_, Rename, TableRow To Variable]

   11/02/2009
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this group. List the MCS groups that contain a compound of interest. Create all the groups with the option limiting each compound to at most one MCS group and present the structures in these groups in a matrix. [Revision: 1 #2.0, 1-2 #2.0, 1-3 #2.0, 1-4 #2.0, 1-5 #2.0] [Requires: Canvas]

[List of nodes: Extract MAE Properties, Row Filter, GroupBy, Column Filter, Java Snippet, Set MAE Properties, Column Combiner, Number To String, Text Viewer, Maximum Common Substructure Search, Group MAE, Compare Ligands, Column Resorter, MAE_to_Smiles, Lookup and Add Columns, Split Collection Column, Sorter, Molecule Reader, Ungroup MAE, Concatenate]

   11/02/2009
Select Diverse Molecules: Pick diverse molecules from a library and inspect the structures. [Revision: #1.1] [Requires: Canvas]

[List of nodes: Dissimilarity Selection _from Matrix_, Generate Pairwise Matrix, Text Viewer, MAE_to_Smiles, Extract MAE Properties, Lookup and Add Columns, Fingerprint Generation, Molecule Reader]

   11/02/2009
Similarity Search: Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Revision: 1 #2.0, 1-2 #2.1] [Requires: Canvas]

[List of nodes: CDK to Molecule, Text Viewer, Molecule Reader, Extract MAE Properties, GroupBy, Sorter, Similarity Matrix _from Molecules_, Concatenate, RowID, Transpose, Java Snippet, Inject Variables _Data_, Row Iterator Loop Start, Column Filter, Loop End, TableRow To Variable, Rename, Row Filter, Structure Sketcher, Lookup and Add Columns]

   11/02/2009
Substructure Search: Sketch a molecule and search the target molecules against that query. Report the compounds that don't pass all the REOS filters. [Revision: #2.0] [Requires: Canvas]

[List of nodes: CDK to Molecule, Text Viewer, Molecule Reader, REOS Filter, Substructure Search, Structure Sketcher]

   11/02/2009
Docking / Docking Post-processing
Align Binding Sites and Protein preparation: Align the binding site of PDB structures and prepare them for further calculations. [Revision: #1.0] [Requires: Impact]

[List of nodes: Molecule Reader, Assign Bond Orders, Add Hydrogens, Run Maestro, Align Binding Sites, Delete Atoms, Impref, Prime Fix, Protein Assignment]

   11/02/2009
Docking and Scoring: Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-process them with Prime MM-GBSA. Build two different MLR models for predicting the Glide score. [Revision: 1 #1.1, 1-2 #1.1] [Requires: Glide, LigPrep, Prime, QikProp]

[List of nodes: Prime Fix, Column Filter, QikProp, Linear Regression _Learner_, Glide Grid Reader, Run Maestro, Row Filter, LigPrep, Linear Regression _Predictor_, MAE_to_Smiles, Extract MAE Properties, XLogP, Text Viewer, Prime MM_GBSA, File Reader, RRHO Entropy, Scatter Plot, Lookup and Add Columns, SMILES to CDK, Glide Ligand Docking]

   11/02/2009
Ensemble Docking: Dock ligands into multiple conformations of the binding site and report the best pose per ligand. [Revision: #2.0] [Requires: Glide]

[List of nodes: GroupBy, Sorter, Glide Ligand Docking _Multiple_, Glide Multiple Grid Reader, Glide Multiple Ligand Docking, Java Snippet, Text Viewer, Run Maestro, Molecule Reader, Ungroup MAE, Extract MAE Properties, Multiple Glide Grid Reader]

   11/02/2009
Induced Fit Docking Protocol: Run the default Induced Fit Docking protocol or customize the individual stages. Visual representation of the protein-ligand complexes (molecular representation, color, mutations) can be set before displaying the results in Maestro. [Revision: 1 #2.0, 1-2 #2.0] [Requires: Prime, Glide]

[List of nodes: Sort and Filter, Extract MAE Properties, Text Viewer, Sorter, Run Maestro, Prime Fix, Molecule Reader, One step docking, Column Reorder, Side Chain Remover, Induced Fit Docking, Prime Induced Fit, Math Formula]

   11/02/2009
Loop Over Docking Parameters: Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Revision: #2.2] [Requires: Glide]

[List of nodes: Cell Splitter, Rename, Row Filter, Column Filter, GroupBy, Java Snippet, Inject Variables _Data_, Loop End, Glide Multiple Ligand Docking, Row To Variable Loop Start, Chemistry External Tool 0_1, Molecule Reader, Ungroup MAE, Text Viewer, Glide Grid Reader, Extract MAE Properties]

   11/02/2009
Validate Docking Parameters with Active and Inactive Compounds: Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an enrichment plot and a ROC curve. Do the same comparisons after post-processing the results with Prime MM-GBSA. [Revision: 1 #2.0, 1-2 #2.0, 1-3 #2.1] [Requires: Glide, LigPrep, Prime]

[List of nodes: Extract MAE Properties, Molecule Reader, GroupBy, Glide Grid Reader, Sorter, Run Maestro Command, Row Filter, Number To String, Math Formula, Glide Sort Results, Glide Ligand Docking, Prime MM_GBSA, Concatenate, Java Snippet, ROC Curve, Text Viewer, Run Maestro, Column Filter, Enrichment Plotter, LigPrep, Set MAE Properties, Column Reorder, View CSV]

   11/02/2009
Virtual Screening: Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, SP, XP). [Revision: 1 #1.1, 1-2 #1.1] [Requires: Glide, Qikprop, LigPrep]

[List of nodes: Text Viewer, LIGPREP, QIKPROP, Row Filter, Molecule Writer, Molecule Reader, Row Sampling, Extract MAE Properties, Sorter, Property Filter _Propfilter_, Glide Grid Reader, LigPrep, QikProp, MAE_to_Smiles, Run Maestro, Glide Ligand Docking]

   11/02/2009
Molecular Mechanics
Compare Conformantional Search Methods: Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [Revision: #1.2] [Requires: MacroModel, ConfGen]

[List of nodes: ConfGen, Extract MAE Properties, Conformational Search, Joiner, Column Filter, Rename, Molecule Reader, MAE_to_Smiles, Text Viewer, Chemistry external tool 1:1]

   11/02/2009
Homology Modeling
Model Building: Read a sequence, search for possible templates, look for relevant ones and build the homology model. [Revision: #1.2] [Requires: Prime]

[List of nodes: Alignment Writer, Prime Build Homology Model, Extract MAE Properties, Ungroup MAE, Text Viewer, BLAST, Run Maestro, Sequence Reader, Molecule Writer, Column Resorter, Row filter]

   11/02/2009
Pharmacophore Modelling
Phase Shape Screening: Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. [Revision: #2.0] [Requires: Phase]

[List of nodes: Phase Shape, Concatenate, Extract MAE Properties, Molecule Reader, Sorter, Run Maestro]

   11/02/2009
Phase Database Screening: Prepare a set of ligands and create a Phase database. Screen this database against several hypotheses using two sets of parameters. Compare the results based on the number of hits found and inspect the hits in Maestro. [Revision: #2.0] [Requires: Phase, LigPrep]

[List of nodes: Sorter, Hypothesis Reader, Text Viewer, ConfGen, Phase DB Creation, Ungroup MAE, Phase DB Query, Molecule Reader, Concatenate, Extract MAE Properties, Row Filter, Column Filter, Run Maestro, CSV Writer, LigPrep, Molecule Writer]

   11/02/2009
Phase Hypothesis Identification: Find common pharmacophores for four ligands using hypotheses with four to seven points. Export the best hypotheses found. [Revision: 1 #1.1, 1-2 #1.1] [Requires: Phase, Impact]

[List of nodes: ]

   11/02/2009
KNIME Workbench
GroupBy Use-cases: Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: maximum/minimum, unique count, unique concatenate, set, and list. [Revision: 1 #2.0, 1-2 #2.0]

[List of nodes: Table Reader, Text Viewer, Sorter, Cell Splitter, Split Collection Column, GroupBy, Rename, String_to_Type]

   11/02/2009
General Tools
Ensure Molecule Title Uniqueness: Ensure unique molecule titles (using the KNIME RowID or the Schrödinger dedicated node). This is useful in the context of Canvas. [Revision: #2.1]

[List of nodes: Set Molecule Title, RowID, Similarity Matrix _from Molecules_, Molecule Reader, Extract MAE Properties]

   11/02/2009
Group Looper: Illustrate how to iterate over structures in the input table with two different looper implementations. Extract the second lowest energy conformer of each molecule after a conformational search. [Revision: #2.1]

[List of nodes: Text Viewer, Row Filter, Row Iterator Loop Start, Loop End, Ungroup MAE, Table Reader, Inject Variables _Data_, Row To Variable Loop Start]

   11/02/2009
Output Column Structure Options Philosophy: Illustrate the Output column structure options (output only, input plus output, and output replaces input). The workflow also demonstrates a potential workaround for nodes that don't have the output column structure options. [Revision: #2.1] [Requires: Impact]

[List of nodes: Text Viewer, Extract MAE Properties, Unique Smiles, Molecule Reader, Premin, Set MAE Properties]

   11/02/2009
Protein Structure Alignment: Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole structure (using the 'Protein Structure Alignment' node). [Revision: #2.0]

[List of nodes: Concatenate, Get PDB, Molecule_to_MAE, Delete Atoms, Run Maestro, Protein Structure Alignment, Align Binding Sites]

   11/02/2009
Run Maestro Command Node Use-cases: The Run maestro command node is used to alter the formal charge of some atoms defined by an ASL and for altering the structure rendering before inspection of the OPLS partial charges. [Revision: #2.0]

[List of nodes: Delete Atoms, Run Maestro, MacroModel Single Point Energy, Run Maestro Command, Molecule Reader, Add Hydrogens]

   11/02/2009


Important Notes

The calculation parameters in the example workflows have been chosen so as to minimize the calculation time, not to produce scientifically valid results.

The workflows have been executed and saved with the intermediate data. You can reset all the nodes in a particular workflow except for the first node, if you wish to execute the workflow using the example data. You only need to download the example input data if you want to execute the whole workflow from scratch.

Include optional example data in the download.

NOTICE: THE WORKFLOWS ON THIS WEB SITE HAVE BEEN GENERATED BY SCHRÖDINGER OR BY USERS OF SCHRÖDINGER SOFTWARE. THE WORKFLOWS ARE PROVIDED FREE OF CHARGE. THE WORKFLOWS ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, AND MAY NOT BE ERROR FREE. SCHRÖDINGER AND THE AUTHORS OF THESE WORKFLOWS DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL SCHRÖDINGER OR THE AUTHORS OF THESE WORKFLOWS BE LIABLE FOR SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND.
I have read the Important Notes above. You must check this box before downloading.

Download Now


Installation Instructions

After you have downloaded Schrodinger_Workflows_Download.zip, you can import the workflows by following these steps:

  • In the KNIME Workbench, choose File->Import KNIME Workflow...
  • In the Import panel, click "Select archive file" and then Browse...
  • Browse to and select the Schrodinger_Workflows_Download.zip file
  • Click Finish

To install workflow example data (if included in the download):

  • On Linux
    • Move the Schrodinger_Workflows_Download.zip file into an empty directory and unzip the file:

      unzip Schrodinger_Workflows_Download.zip

    • Move the knime_workflow_example_data.zip file into /tmp and extract it:

      mv knime_workflow_example_data.zip /tmp/
      cd /tmp/
      unzip knime_workflow_example_data.zip
  • On Windows:
    • Move the Schrodinger_Workflows_Download.zip file into an empty directory and unzip the file.
    • Choose a directory in which to unzip knime_workflow_example_data.zip.
    • The example workflows provided in the Schrodinger_Workflows_Download.zip were saved under Linux, and are configured to use example data in subdirectories under /tmp/knime_workflow_example_data/. Since there is no /tmp/knime_workflow_example_data/ directory under Windows, you will need to reconfigure the nodes in the workflows to point to the location where you have unzipped the knime_workflow_example_data.zip file.
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