Select Description Updated
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. [1 (2.1), 1-2 (1.2), 1-3 (2.3), 1-4 (2.6)] [Requires: Canvas]
04/01/2011
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. [1 (3.6), 1-2 (3.6)] [Requires: Canvas]
04/01/2011
Maximum Common Substructure Search (MCS) : Create all possible MCS groups and list the groups identified. Inspect the compounds in a given group and list the compounds not included in that 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. [1 (2.1), 1-2 (2.1), 1-3 (2.1), 1-4 (2.1)] [Requires: Canvas]
04/01/2011
Select Diverse Molecules : Pick diverse molecules from a library and inspect the structures. [1 (1.1)] [Requires: Canvas]
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. [1 (2.0), 1-2 (3.6)] [Requires: Canvas]
04/01/2011
Substructure Search : Sketch a molecule and search the target molecules against that query. Report the compounds that don't pass all the REOS filters. [1 (2.0)] [Requires: Canvas]
11/02/2009
Docking / Docking Post-processing
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. [1 (1.1), 1-2 (1.3)] [Requires: Glide, LigPrep, Prime, QikProp]
04/01/2011
Ensemble Docking : Dock ligands into multiple conformations of the binding site and report the best pose per ligand. [1 (2.1)] [Requires: Glide]
05/26/2010
Loop Over Docking Parameters : Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [1 (2.3)] [Requires: Glide]
04/01/2011
Protein Preparation and Glide Grid Generation : Align the binding site of PDB structures, prepare them and generate the Glide grids. Analyze the protein-ligand complex composition and display the ligand 2D structures in 2D. [1 (3.1), 1-2 (3.1), 1-3 (3.1)] [Requires: Impact and Glide]
06/12/2011
Validate Docking Parameters : 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. [1 (2.0), 1-2 (2.0), 1-3 (2.1)] [Requires: Glide, LigPrep, Prime]
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). [1 (1.1), 1-2 (1.2)] [Requires: Glide, QikProp, LigPrep]
11/02/2009
Chemistry External Tool Use-cases : The Chemistry external tool nodes are used to parse a log file with basic shell commands and run the utility CanvasConvert and Phase Shape backend with specific options. [1 (3.5)] [Requires: Phase]
12/23/2010
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. [1 (2.1)] [Requires: Maestro]
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. [1 (2.4)] [Requires: MacroModel, Impact]
04/01/2011
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). [1 (2.0)] [Requires: Maestro]
11/02/2009
Python Script Node Use-cases : The Python Script nodes are used to extract ring properties, start PyMOL from KNIME, run a MacroModel conformational search with specific
parameters, and measure distances between atoms for the conformer generated. [1 (4.1)] [Requires: MacroModel]
06/13/2011
Run Maestro Command 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 [1 (2.1)] [Requires: Maestro]
04/01/2011
Induced Fit Docking Protocol : Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular representation, color, mutations) can be set before displaying the results in Maestro. [1 One step (2.9), 1-2 Individual steps (2.9)] [Requires: Glide, Prime]
05/26/2010
Model Building : Read a sequence, search for possible templates, look for relevant ones, build an homology model including the largest ligand and compare it to the template structure. Run side chain sampling in the binding site. [1 (3.7), 1-2 (4.0)] [Requires: Prime]
04/01/2011
Library Enumeration : Libraries are created by substitution of one or several attachments on a
core structure with fragments from reagent compounds. A unique identifier
is assigned to each generated compound.
[1 (4.2), 1-2 (4.2), 1-3 (4.2)] [Requires: CombiGlide]
06/13/2011
Metanodes (require KNIME 2.4)
SiteMap : A set of PDB structures are prepared and SiteMap is run around the largest
ligand of each structure.
[(4.5)] [Requires: SiteMap]
10/18/2011
Run Maestro 1:1 use-cases : Uses the Run Maestro 1:1 metanode to alter some structures in the middle
of a workflow, pick residues to sample in a binding site, pick atoms to
make measurements or select a core for library enumeration.
[(4.5)] [Requires: Prime, CombiGlide]
09/28/2011
Compare ConfSearch Methods : Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [1 (1.2)] [Requires: MacroModel, ConfGen]
11/02/2009
Phase Shape : Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. [1 (2.0), 1-2 (4.0)] [Requires: Phase]
11/02/2009
Phase Hypothesis Identification : Find common pharmacophores for four ligands using hypotheses with four to seven points. Export the best hypotheses found. [1 (1.2), 1-2 (1.1)] [Requires: Phase, Impact]
11/02/2009
Phase Screening : Screen a file against one hypothesis. 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. [1 (2.3), 1-2 (4.1), 1-3 (2.9)] [Requires: Phase, LigPrep]
06/12/2011
Conformational Search and QM Refinement : Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer template is used to present the results. [1 (4.1), 1-2 (4.1), 1-3 (4.1)] [Requires: MacroModel, Jaguar]
06/12/2011
Vendor database preparation : The workflow labels compounds from a single
vendor, prepares and filters them by various criteria. It is based on:
Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; Norman, D.;
Lockey, P.M.; Roach, A.G. J. Med. Chem., 2004, 47, 3962.
[1 (4.1), 1-2 (4.1), 1-3 (4.1)] [Requires: Canvas]
05/17/2011
Workflows in the current workspace : Lists the latest modified workflows in the current workspace or workflows
containing specific nodes. It can be used to compare several versions of a
workflow or find a workflow that can be used as a basis to create a
new one.
[1 (4.1)] [Requires: ]
06/14/2011
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. [1 (2.0), 1-2 (2.0)] [Requires: Maestro]
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. [1 (2.3)] [Requires: Maestro]
04/01/2011
Unpivot : Use a loop to unpivot the data. See also the Similarity search workflow example where the Unpivot node is used instead. [1 (2.1)] [Requires: Canvas]
04/01/2011
