days
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 (2.7)] [Requires: Canvas]
03/17/2012
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 (3.7), 1-2 (3.7)] [Requires: Canvas]
03/17/2012
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. [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 : Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters.
[1 (2.0), 1-2 (5.0)] [Requires: Canvas]
03/17/2012
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. [(2.3)] [Requires: Glide]
03/17/2012
Loop Over Docking Parameters : Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [ (2.7)] [Requires: Glide]
03/17/2012
Protein Preparation and Glide Grid Generation : Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and
display the ligand structures in 2D. [1 (3.1), 1-2 (3.1), 1-3 (5.0)] [Requires: Glide]
03/17/2012
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
Validate docking parameters with KNIME - Maestro connectors : Start Maestro structure exchange with KNIME server so as to perform some steps interactively in Maestro (highlighted in orange). Extract co-crystallized ligands from PDB structures. Prepare and concatenate them with known active, and inactive compounds. Compare the enrichment curves after docking and post-processing with Prime MM-GBSA. [1 (5.0), 1-2 (5.0)] [Requires: Glide, LigPrep, (Prime)]
03/17/2012
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 can be used to parse a log file with basic shell commands, run a utility like CanvasConvert, run Phase Shape backend
with specific options or launch PyMOL. [(3.7)] [Requires: Maestro, (Phase)]
03/17/2012
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. [(2.1)] [Requires: Maestro, (Canvas)]
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 yet. [(2.4)] [Requires: MacroModel, Glide]
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). [(2.0)] [Requires: Maestro]
11/02/2009
Python Script Node Use-cases : The Python Script nodes are used to extract ring properties, run a MacroModel conformational search with specific parameters, and measure distances between atoms for the conformer generated. [(4.3)] [Requires: MacroModel]
03/17/2012
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. [(2.1)] [Requires: Maestro, (Macromodel)]
04/01/2011
Split and align multimers : Split protein multimers by chain ID and align binding sites.
[1 (5.0), 1-2 (5.0), 1-3 (5.0)] [Requires: Maestro]
03/17/2012
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 new compound.
[1 (4.2), 1-2 (4.9), 1-3 (4.9)] [Requires: CombiGlide]
03/17/2012
Glide grid writer : A protein binding site conformation is manually alterated, the Glide grid
generated and written to disk.
[(5.0)] [Requires: Glide]
03/17/2012
Jaguar pKa : Evaluate the pK a of specified atoms using Jaguar.
[(5.0)] [Requires: LigPrep, Jaguar]
03/17/2012
Run Maestro 1:1 use-cases : Use the Run Maestro 1:1 metanode to alter some structures in the middle of a workflow, pick residues to sample in a binding site. [(4.5)] [Requires: Prime]
09/28/2011
Run PyMOL : Display structures in PyMOL. Run PyMOL commands on structures.
[(5.0)] [Requires: Maestro, PyMOL]
03/17/2012
SiteMap : A set of PDB structures is prepared and possible binding sites identified with SiteMap.
[(4.9)] [Requires: SiteMap]
03/17/2012
Desmond simulation : Prepare a system and run a Desmond MD simulation. Then some frames are extracted and analyzed in terms of hydrogen bond network and atom distance.
[1 (5.0), 1-2 (5.0), 1-3 (5.0)] [Requires: Desmond]
03/17/2012
Compare Conformational Search Methods : Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [(1.2)] [Requires: MacroModel, ConfGen]
11/02/2009
Conformational search and post-processing : Extract ligands from PDB structures, run a ConfGen and compare the conformations generated in terms of RMSD and intramolecular distance. Run the same analysis to compare 2 ConfGen modes.
[1 (5.0), 1-2 (5.0), 1-3 (5.0)] [Requires: ConfGen]
03/17/2012
Phase Hypothesis Identification : Find common pharmacophores for four ligands using hypotheses with four to seven points. Export the best hypotheses found. [1 (1.4), 1-2 (1.1)] [Requires: Phase]
03/17/2012
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 (4.2), 1-3 (3.4)] [Requires: Phase]
03/17/2012
Phase Shape Screening : Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. [1 (2.0), 1-2 (4.0)] [Requires: Phase Shape]
11/02/2009
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 (2.9), 1-2 (3.1)] [Requires: Glide, Prime]
03/17/2012
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 a side chain sampling and a minimization of the binding site. [1 (3.7), 1-2 (4.6)] [Requires: Prime]
03/17/2012
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 (4.3), 1-3 (4.3)] [Requires: MacroModel, Jaguar]
03/17/2012
ESP charges : Run a semi-empirical and a Jaguar optimization. Then calculate and display in Maestro the ligand ESP charges.
[(5.0)] [Requires: LigPrep, Jaguar]
03/17/2012
Binding site shape clustering : The binding site shape is analyzed with SiteMap and clustered to generate a receptor structural ensemble. The corresponding Glide grids are generated and used for ensemble docking.
The input structures can also be molecular dynamic snapshots (see the Desmond simulation workflow example).
The workflow runs serially and a parallelized version based on KNIME 2.7 will be added in the future.
See details in:
Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. J. Phys. Chem. B 2012, 116, 6952−6959 and
Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. Chem Biol Drug Des 2012; 80: 182–193
[(5.5)] [Requires: SiteMap, Canvas, (Glide)]
12/07/2012
SiteMap and Glide grid generation : A set of PDB structures is prepared and possible binding sites identified with SiteMap. A Glide grid is generated for each site and used to dock ligands.
[1 (5.0), 1-2 (5.0)] [Requires: SiteMap, Glide]
03/17/2012
Vendor database preparation : The workflow labels compounds from a single vendor, prepares and filters them by various criteria. 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 (4.4), 1-2 (4.4), 1-3 (4.4)] [Requires: Canvas]
03/17/2012
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:]
11/02/2009
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.
[(4.1)] [Requires: Maestro]
06/14/2011
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 (2.5)] [Requires: ]
03/17/2012
Unpivot : Use a loop to unpivot the data. See also the Similarity search workflow
example where the Unpivot node is used instead.
[(2.1)] [Requires:]
04/01/2011
