Below are many useful workflows for performing automation, customization, and scientific augmentation to the Schrödinger Suites. 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.

 

Format: Dec 2021
  • The latest versions of the workflows are available from the KNIME hub or NodePit.
    • You don't have to log in to download individual workflow examples. Drag and drop of workflow groups into the KNIME Analytics Platform works, too.
    • When logged in you can download workflow groups or the whole workflow example KNIME hub space.

 

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ADME
Description Last Updated Release
Atropisomerism:

"ADME properties are calculated with QikProp. The workflow is exported as Computational model in LiveDesign."

11/12/2020 Release 2021-4
Membrane Permeability:

Calculates an estimated passive membrane permeability for a ligand structure by comparing the energy optimized conformations of that ligand in low and high dielectric. 
Calculates the amphipilic moment of positively charged molecules.

5/18/20 Release 2021-4
P450 Site of Metabolism:

 In this workflow P450 Site of Metabolism calculation can be set and run to evaluate a set of ligands for the likely sites of metabolism by 2D6 or 2C9 P450 isoform.

Release 2021-4
QikProp Property Plot:

Plots a set of QikProp molecular properties to compare the structures.

Release 2021-4
Cheminformatics
Description Last Updated Release
AutoQSAR:

Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR nodel to other compounds, with either traditional QSAR methods or DeepChem deep learning methods. [Requires: AutoQSAR]

Release 2021-4
Clustering: 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. [Requires: Canvas] Release 2021-4
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. [Requires: Canvas]

Release 2021-4
Diversity:

 Pick diverse molecules from a library and inspect the structures. [Requires: Canvas]

Release 2021-4
Maximum Common Substructure Search (MCSS):

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. [Requires: Canvas]

Release 2021-4
Similarity:

 Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Requires: Canvas]

Release 2021-4
Substructure:

 Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters. [Requires: Canvas]

Release 2021-4
Docking
Description Last Updated Release
Binding Site:

Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap]
The SiteMap node is used in more complex workflow examples:
- Real work examples - SiteMap and docking
- Real work examples - Binding site shape clustering"

Release 2021-4
Core Constraint:

Compounds are docked with a core constraint using the MCS with the reference ligand.

5/18/2020 Release 2021-4
Covalent Docking:

Dock and covalently binds ligands to the specified reactive residue in the protein target using Michael addition reaction type. [Requires: ProteinPrep, LigPrep]

Release 2021-4
Docking in the Most Similar Binding Site:

Dock the ligands in the most similar protein of a set of structures, based on the comparison with the cocrystallized ligand in each of them.

5/18/2020 Release 2021-4
Ensemble Docking:

 Dock ligands into multiple conformations of the binding site and report the best pose per ligand. [Requires: Glide]

Release 2021-4
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. [Requires: Glide]

Release 2021-4
Loop Over Docking Parameters:

 Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glide]

Release 2021-4
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. [Requires: Glide, LigPrep, Prime]

Release 2021-4
Virtual Screening:

 Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, SP, XP). [Requires: Glide, QikProp, LigPrep]

Release 2021-4
General Tools
Description Last Updated Release
Ensure Molecule Title Uniqueness:

 Ensure unique molecule titles (using the KNIME RowID or the Schrodinger dedicated node). This is useful in the context of Canvas. [Version: 2.1][Requires: Maestro, Canvas]

Release 2021-4
Ligand Alignment:

Align a set of ligand structures flexibly with torsional variation, using a best practices approach to choose the most appropriate method. The ligands can be similar (a congeneric series, for example, or multiple congeneric series with different cores) or diverse.

Release 2021-4
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. [Requires: MacroModel, Glide]

Release 2021-4
Labs
Description Last Updated Release
Parameter Flow Variable Use-cases: Use the parameter flow variables to control command line options not exposed in configuration panel. This is illustrated for the protein preparation, Shape screenling, Macromodel minimization, Molecule reader and other nodes. [Version: 2.7.4][Requires (optionally): (MacroModel, Phase, LigPrep, Prime)][Keywords: Parameter flow variables, Quick form] Release 2021-4
Library Design
Description Last Updated Release
Bioisoster Replacement: Functional groups are replaced with bioisosteres that are available in the literature. Release 2021-4
Library Design Workshop:

Bioisostere and R-group enumeration using custom or predefined isosteres and libraries. Reaction-Based Enumeration to rapidly generate idea molecules with significant diversity and high probability of being synthesizable.

Release 2021-4
R-group Enumeration:

Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds. Unique identifiers are assigned to each new compound. [Requires: Maestro]

Release 2021-4
Reaction-based Enumeration:

 Enumerate structures by substitution of R groups in the reactants and products of a single- or multi-step reaction. Also used for Core hopping. [Requires: -]

Release 2021-4
LiveDesign
Description Last Updated Release
LiveDesign Administration:

Usage examples of the nodes operating on a list of models or protocols to upload, download and verify them.
- Create backup copies of some models before they are updated
- Create a model or protocol copy for testing changes and only visible from a specific project
- Copy from a testing to a production LiveDesigninstance
- Deploy the latest version of the validated models available from the KNIME hub
- Deploy the latest version of the generic KNIME protocols
- Compare 2 versions of a protocol or a model

Release 2021-4
LiveDesign Import and Export:

  Structures and properties are retrieved from LiveDesign. New properties are added to an existing Live report.

Release 2021-4
Related PDB Structures:

PDB structures containing ligands similar to each LiveReport structures are listed. The PDB structure with the most similar ligand is prepared and added to a new column in the LiveReport. New columns are also populated with the Ligprepped ligand and its Epik protonation and tautomeric forms.

Release 2021-4
LiveDesign Models
Description Last Updated Release
ADME:

Calculates ADME properties with QikProp.
Input: Compound structure column
Output column(s): 
- a selection of Qikprop properties

Release 2021-4
Atropisomerism:

It detects atropisomers in input structures. Each rotatable bond is sampled, and energies are calculated. If the energy difference between the lowest and the highest energy states is sufficient and the energy difference between the two lowest energy states is small, then this bond is assumed to be atropisomeric.
Compound stucture as input column
Output column: 
- Label for structures that may be atropisomers

11/12/2020 Release 2021-4
Basic Example:

Adds 2 simple columns to the LiveReport.

11/12/2020 Release 2021-4
Binding Pocket Surface:

Add the binding pocket surface

Release 2021-4
Binding Pose Strain:

Minimizes the binding pose conformation to a local minimum and runs a conformational search to find the global minimum.
Calculates the conformation energy difference between the local and the global minima

11/12/2020 Release 2021-4
Bioisosteres:

Replaces functional groups of each input ligand with bioisosteres, generating all the single replacements.

5/18/2020 Release 2021-4
Cocrystallized Ligands:

Prepares the protein-ligand complexes in the selected column from the LiveReport and extracts the ligand structures and list.

11/12/2020 Release 2021-4
Docking:

Docks the compounds with Glide and changes the rendering of the binding site (atoms displayed, residues labelled and the atom representation) to highlight important residues.
The workflow is uploaded as Computational model in LiveDesign.

5/18/2020 Release 2021-4
Docking and Ligand Strain:

Docks the compounds with Glide, minimizes the binding pose conformation to a local minimum and runs a conformational search to find the global minimum. Calculates the conformation energy difference between the local and the global minima. Aligns the global minimum conformation on the initial binding pose.

11/12/2020 Release 2021-4
Docking and Protein Surface:

Docks the compounds with Glide. Also generates the protein surface and changes the rendering of the binding site (atoms displayed, residues labelled and the atom representation) to highlight important residues.

11/12/2020 Release 2021-4
Docking and Rendering:

Docks the compounds with Glide and changes the rendering of the binding site (atoms displayed, residues labelled and the atom representation) to highlight important residues

11/12/2020 Release 2021-4
Ensemble Docking:

Docks the compounds with Glide in 2 binding site conformations and reports the binding site conformation where it scores the best and the corresponding docking pose.

11/12/2020 Release 2021-4
ESP Surface:

Runs a semiempirical calculation to optimize the ligand geometry and generates the ESP surface.

5/18/2020 Release 2021-4
FEP Analysis:

Extracts simulation quality analysis information from a FEP map column.

11/12/2020 Release 2021-4
Get PDB from FFC and Preparation:

Downloads the structure for the PDB IDs listed in the selected Free Form Column from the LiveReport, optionally prepare the structures, extracts and creates new columns with the structures and corresponding structural information.

11/12/2020 Release 2021-4
Interaction Surface:

Adds the binding pocket interaction surface generated with SiteMap.

Release 2021-4
Ligand Alignment by Shape with a Corystallized Reference:

Aligns ligands on a rigid template structure using Shape screening.

Release 2021-4
Ligand Alignment by Shape with a Flexible Reference:

Aligns ligands on a reference structure treated flexibly as well, using Shape screening.

Release 2021-4
Ligand Alignment with a Cocrystallized Reference:

Aligns the structures on a reference ligand kept rigid using align_ligands utility.

Release 2021-4
Ligand Alignment with a Pharmacophore:

Input column: Compound structures in the LiveReport
Configuration: The pharmacophore hypothesis file can be changed on LiveDesign admin page or from the Parametrize model panel.
Aligns the ligands against a pharmacophore hypothesis using Phase.
Output column(s) in the LiveReport: 
- 3D ligand alignment on the pharmacophore hypothesis
- Matched sites
- alignment score

Release 2021-4
Ligand CNS Desirability Plot:

Generates radar plots for the CNS desirability MPO properties.

11/12/2020 Release 2021-4
Ligand CNS Desirability Range Plot:

Generates radar plots of the CNS desirability MPO properties and the number of rotatable bonds with the optimal property range.

11/12/2020 Release 2021-4
Ligand Property Radar Plot:

Generates a radar plot of the QikProp properties selected in the workflow.

5/18/2020 Release 2021-4
List Protocols and Models:

List LiveDesign protocols, models and corresponding parametrized models. Consider archiving some models or unarchive them if needed.

Release 2021-4
Low Energy Conformation:

Runs a MacroModel or ConfGen conformational search structures prepared with LigPrep

5/18/2020 Release 2021-4
My Workflow Running on a KNIME Server:

Input column: Compound structures in the LiveReport
Runs another workflow remotely on a KNIME server.

Release 2021-4
Protonation Forms:

Generates protonation forms with Epik and adds a new column with the structure of the most probable form.

Release 2021-4
Random Forest:

Reports the predictions of a pregenerated random forest QSAR model run on physicochemical properties generated with QikProp from the LiveReport compound structures.
The QSAR file can be changed on the model admin page or from the Parametrize model panel.

11/12/2020 Release 2021-4
Related PDB Structures:

PDB structures containing ligands similar to each LiveReport structures are listed. The PDB structure with the most similar ligand is prepared and added to a new column in the LiveReport. New columns are also populated with the Ligprepped ligand and its Epik protonation and tautomeric forms.

Release 2021-4
Materials Science
Description Last Updated Release
Periodic Descriptors:

Generates descriptors that can be used in a machine learning model to predict bulk properties such as ionic conductivity, band gap, bulk modulus, formation energy etc.

Release 2021-4
Molecular Dynamics
Description Last Updated Release
Binding Pose Metadynamics:

Various binding configurations of a single ligand in a single binding site are ranked.

Release 2021-4
FEP Analysis:

An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including errors and conversion checking). So results can be labeled, triaged, filtered, and extra data can be merged.

Release 2021-4
Ligand alignment MD refinement:

A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime and the RMSDs are reported to assess the pose stability. 
The workflow can be used to refine for instance on a docking based alignment to prepare the input of a FEP calculation.

Release 2021-4
MD 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. [Requires: Desmond][Keywords: Molecular dynamics simulation, trajectory, snapshots, jobcontrol, distance, hydrogen bond, atom selection]

Release 2021-4
Molecular Mechanics
Description Last Updated Release
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. [Version: 1.7][Requires: MacroModel, ConfGen][Keywords: conformational search, parsing]

Release 2021-4
Macrocyclization:

Starting from a linear compound macrocyclizations are created, the conformations sampled and compared for a cocrystallized ligand.

5/18/2020 Release 2021-4
Pharmacophores
Description Last Updated Release
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. [Version: 2.4.2][Requires: Phase]

Release 2021-4
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. Commands to run the workflow in batch. [Version: 4.0][Requires: Shape Screening]

Release 2021-4
Protein Modeling
Description Last Updated Release
BioLuminate Residue Scanning:

 The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the stability and affinity of the mutated structures. Additionally, you can gain access to the latest command-line only functionalities of the tool (e.g., to control Prime loop sampling options), run affinity maturation and aggregation calculations that can be used to compare the mutants. [Version: 2.8.0 Requires: BioLuminate]

Release 2021-4
Build Antibody Models:

Several antibody models are built using Biolumianate tool starting from the heavy and light chain sequences.

Sequences can be read from an XLS spreadsheet. Post-translational modifications and protein descriptors are calculated for each model and the latter can be used as input to BioQSPR.

Release 2021-4
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. [Version: 3.1][Requires: Glide, Prime]

Release 2021-4
Missing loop refinement:

Refine all the loops added using 'Fill loops' option in the Protein Preparation node

Release 2021-4
Model Building: Read an amino acid sequence, search for possible templates, look for relevant ones, build a 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. Release 2021-4
Model Building on a Template: Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is analyzed. A raytrace image of the model is also created. [Requires: Prime, Glide, SiteMap, PyMOL] [Keywords: binding site, homology modeling, grid generation] Release 2021-4
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). [Version: 2.0.5][Requires: Maestro]

Release 2021-4
Reactive Protein Residues:

Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures.

Release 2021-4
Sequence Converter:

 Metanode to run the Sequence converter utility. [Requires: -] [Keywords: Protein]

Release 2021-4
Split and Align Multimers:

 Split protein multimers by chain ID and align binding sites. [Version: 5.0][Requires: Maestro]

Release 2021-4
Structure Reliability Report:

Reports various metrics that indicate the reliability or quality of a protein structure, and in particular, X-ray structures of proteins.

5/18/2020 Release 2021-4
WaterMap:

 A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.

Release 2021-4
Quantum Mechanics
Description Last Updated Release
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. [Requires: MacroModel, Jaguar]

Release 2021-4
ESP Charges:

 Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Version: 7.0][Requires: LigPrep, Jaguar]

Release 2021-4
Jaguar pKa:

 Evaluate the pKa of specified atoms using Jaguar. [5.3][Requires: LigPrep, Jaguar][Keywords: Quantum mechanics, pKa, parameter flow variables]

Release 2021-4
Jaguar pKa:

 Evaluate the pKa of specified atoms using Jaguar. [5.3][Requires: LigPrep, Jaguar][Keywords: Quantum mechanics, pKa, parameter flow variables]

Release 2021-4
QM Conformational Search:

 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. [Requires: MacroModel, Jaguar]

Release 2021-4
QM Descriptors:

It generates a series of jobs and harvests molecular (including Dipole Moment, HOMO/LUMO, isodensity surface contributions, Internal energy, energy components, enthalpy, entropy and Gibbs free energy contributions) and atomic descriptors (including charges, Fukui indices, electrostatic potential, NMR shielding, spin densities).

Release 2021-4
Quantum Mechanical Properties:

 Calculate the molecular orbitals and vibrational frequencies. [Version: 6.0] [Requires: LigPrep, Jaguar][Keywords: quantum mechanics, semi-empirical, parameter flow variables, quick form nodes]

Release 2021-4
Semiempirical Optimization:

 Run semi-empirical NDDO quantum chemical optimization and generate surface properties. [6.0][Requires: LigPrep, Maestro]

Release 2021-4
Tautomer Prediction: Generate the lowest energy tautomers or conformers (or both) for a set of structures, with optional protonation or deprotonation. It ensures that the structures you use for some other calculation are performed on the lowest energy tautomer or conformer. Using the lowest energy structure is important for FEP+ calculations and for Jaguar pKa calculations, for example. Release 2021-4
Real World Examples
Description Last Updated Release
Binding Site Shape Clustering:

 Analyze a set of PDB structures (or a molecular dynamics trajectory) with SiteMap to characterize frames for possible binding sites. Performed volume clustering on each Sitemap result to produce an ensemble of binding sites. Generate receptor grids for ensemble docking with Glide.

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

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

[Version: 6.1][Requires: SiteMap, Canvas, Glide][Keywords: binding site volume, clustering, docking, molecular dynamics]

Release 2021-4
Cocrystallized Ligand Redocking: Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized ligands are rescored with Glide or Prime mm-gb/sa or redocked and the corresponding RMSD is measured. This workflow is derived from the work published by Paulette Greenidge from Novartis in: Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Sherman, W.; J. Chem. Inf. Model. 2014, 54(10), 2697–717 MM/GBSA binding energy prediction on the PDBbind data set: Successes, failures, and directions for further improvement. Greenidge, P. A.; Kramer, C.; Mozziconacci, J.C.; Wolf, R.M.; J. Chem. Inf. Model. 2013, 53(1), 201–9 [Requires: Glide, LigPrep, Prime] Release 2021-4
Database Preparation:

 Label compounds from a single vendor. Prepare and filter compounds by various criteria.

Release 2021-4
MMP FEP Input Preparation:

This workflow takes as inputs: a list of PDB structure IDs, corresponding cocrystallized ligand and Matched Molecular Pair smiles. It downloads the biological units, runs the protein-ligand complex preparation and checking. The ligand structures are extracted, the MMP created and the FEP calculation input file generated.

5/18/2020 Release 2021-4
Sitemap and Glide Grid Generation:

 Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock ligands. [Version: 5.4][Requires: SiteMap, Glide][Keywords: binding site, ensemble docking, grid generation, druggability]

Release 2021-4
Scripting
Description Last Updated Release
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. It is also illustrated how to use it to run third party tools. [Version: 2.4.2][Requires: MacroModel][Keywords: Python, scripting]

Release 2021-4
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. [Requires: Maestro, Macromodel]

Release 2021-4
Server
Description Last Updated Release
AutoQSAR:

Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR nodel to other compounds, with either traditional QSAR methods or DeepChem deep learning methods.

Release 2021-4
Tools
Description Last Updated Release
Batch Execution:

 Run workflows using the simplified batch execution wrapper script.

Release 2021-4
Debugging:

Runs various test tools and gather information that help diagnosing installation issues or node failures.

5/18/2020 Release 2021-4
Installation Script and Checking:

 The Setup Diagnosis node reports possible problems in the plugin installation and set-up. KNIME_batch.py script is run to install KNIME features and update Schrodinger extensions in an existing or new KNIME installation.

Release 2021-4
Jobcontrol:

The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It can also be used to kill some jobs. It can be used in combination with the Postmortem node to generate diagnosis summary files for problematic calculations.

Release 2021-4
Workflows in the Current Workspace:

 Lists the latest modified workflows in the current workspace or lists workflows containing specific nodes to assist in finding and comparing workflows. Applied on the Schrodinger and KNIME.org workflow examples. [Version: 5.9][Keywords: workflows, workspace, nodes, size, date]

Release 2021-4
Visualization
Description Last Updated Release
KNIME-Maestro Connector Node Use-cases:

 Uses the KNIME-Maestro connector (replacing the Run Maestro 1:1 metanode) to alter some structures in the middle of a workflow, pick residues to sample in a binding site. [Requires: Prime][Keywords: Maestro commands, scripting]

Release 2021-4
Run Maestro and Run Maestro Command:

 Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro, this selection is used to build an ASL. [Version: 3.0.0][Requires: Maestro]

Release 2021-4
Run PyMOL:

 Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL][Keywords: PyMOL, visualization]

Release 2021-4
Workbench
Description Last Updated Release
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. [Version: 2.5]

Release 2021-4
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. [Version: 2.0]

Release 2021-4
Text Cell Parsing:

Parses a text cell into independent rows and columns that can be postprocessed or visualized more easily.

5/18/2020 Release 2021-4
Unpivot:

 Use a loop to unpivot the data. [Version: 2.1]

Release 2021-4
_Nodes
Description Last Updated Release
Chemistry External Tool Node Use-cases:

 The Chemistry external tool nodes can be used to parse a log file with basic shell commands, run Schrödinger utilities or backends with specific options. Quick form nodes can be used to create a configuration panel for this node. [Requires: Maestro, (Phase, MacroModel)]

Release 2021-4
Conformer Cluster:

 Clusters conformers based on Cartesian or torsional RMSD. [Version: 2.9.0][Requires: Maestro, (ConfGen)]

Release 2021-4
Epik:

 Predicts ligand states with Epik and reports the ionization form matrix. Generates with LigPrep minimized ionization-tautomeric forms ready to be docked. [Version: 2.9.0][Requires: Epik, LigPrep]

Release 2021-4
Multiple Sequence Viewer:

Opens the Multiple Sequence Viewer panel to visualize sequences or edit an alignment. [Requires: Maestro]

Release 2021-4
Readers and Writers:

 Reader and write structure files. Read a list of PDB files from a directory. [Version: 3.0.0][Requires: Maestro]

Release 2021-4
Tools:

 Extract the atom-level properties to list the PDB conversion problems. [Version:3.2.0] [Requires: -]

Release 2021-4
Workbench Nodes:

Most commonly used workbench nodes. [Requires: -]

Release 2021-4

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.

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.

 

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