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Schrödinger
Miscellaneous Cheminformatics I/O LiveDesign Utilities Docking and Scoring Converters Molecular Mechanics Protein Preparation and Refinement
  1. Go to item
    Node / Manipulator
    Glide Ligand Docking
    Schrödinger Docking and Scoring
    Glide ligand docking jobs require a set of previously calculated receptor grids and one or more ligand structures. Preparation of…
    1
    schroedinger
  2. Go to item
    Node / Manipulator
    Split by Structure
    Schrödinger Miscellaneous Structure Manipulation
    Split structures by chain, molecule, or residue. Backend implementation $SCHRODINGER/run split_structure.py
    1
    schroedinger
  3. Go to item
    Node / Manipulator
    2D Sketcher
    Schrödinger Labs
    Opens 2D Sketcher Backend implementation $SCHRODINGER/utilities/2d_sketcher
    0
    schroedinger
  4. Go to item
    Node / Manipulator
    Add Hydrogens
    Schrödinger Miscellaneous Structure Manipulation
    Adds hydrogen atoms to produce an all-atom structure. Backend implementation utilities/applyhtreat The command line tool applyhtr…
    0
    schroedinger
  5. Go to item
    Node / Manipulator
    Align Binding Sites
    Schrödinger Miscellaneous Utilities
    +1
    This script performs a pairwise superposition of multiple structures using the C-alpha atoms of selected residues. The reference …
    0
    schroedinger
  6. Go to item
    Node / Source
    Alignment Reader
    Schrödinger I/O
    Read alignment files in FASTA and Maestro format. The input format is determined by the file extension. Note that alignments are …
    0
    schroedinger
  7. Go to item
    Node / Sink
    Alignment Writer
    Schrödinger I/O
    Write alignments to a file in FASTA and Maestro format. The output format is determined by the file extension. Backend implementa…
    0
    schroedinger
  8. Go to item
    Node / Manipulator
    Assign Bond Orders
    Schrödinger Miscellaneous Utilities
    +1
    Assigns double and triple bonds to input structures based on molecular geometry (bond length, bond angles, and dihedral angles). …
    0
    schroedinger
  9. Go to item
    Node / Learner
    AutoQSAR Build Model
    Schrödinger Cheminformatics Modeling
    Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR model to other compounds. Descriptor data an…
    0
    schroedinger
  10. Go to item
    Node / Predictor
    AutoQSAR Predict
    Schrödinger Cheminformatics Modeling
    Choose structures to make predictions for and the model to apply. When the job finishes, the structures with the predicted values…
    0
    schroedinger
  11. Go to item
    Node / Manipulator
    BLAST
    Schrödinger Protein Preparation and Refinement
    Search a protein sequence database using BLAST Note: To enable web-based searching, please ensure the option "Allow use of web se…
    0
    schroedinger
  12. Go to item
    Node / Other
    Batch Test
    Schrödinger Miscellaneous Tools
    Tests this workflow in batch execution. Backend implementation KNIME_batch.py
    0
    schroedinger
  13. Go to item
    Node / Learner
    Bayes Classification Model Building
    Schrödinger Cheminformatics Modeling
    Build a Bayes model from binary or continuous training data that can then be applied to other data sets. Both training set and te…
    0
    schroedinger
  14. Go to item
    Node / Predictor
    Bayes Classification Prediction
    Schrödinger Cheminformatics Modeling
    Predict the dependent variable Y for a set of structures using a previously built Bayes model and the required independent X vari…
    0
    schroedinger
  15. Go to item
    Node / Manipulator
    Bioisostere Replacement
    Schrödinger Library Enumeration
    Replace functional groups on a set of ligands with the corresponding bioisosteres, generating all single replacements. Note: In c…
    0
    schroedinger
  16. Go to item
    Node / Manipulator
    Boltzmann Population
    Schrödinger Miscellaneous Utilities
    Calculate a Boltzmann population for selected entries and add it as a property. This calculates the Boltzmann energy (property 'r…
    0
    schroedinger
  17. Go to item
    Node / Source
    CSV Reader (deprecated)
    Schrödinger
    Reads multiple text files, with each file having options for loading. To remove files from the list select the file and press the…
    0
    schroedinger
  18. Go to item
    Node / Manipulator
    Canvas Fingerprint Generation
    Schrödinger Cheminformatics Fingerprint Based Tools
    Generate molecular fingerprints Backend implementation utilities/canvasFPGen canvasFPGen is used to implement this node.
    0
    schroedinger
  19. Go to item
    Node / Source
    Canvas Fingerprint Reader
    Schrödinger I/O
    Reads Binary Canvas Fingerprints into one cell. Backend implementation fpinfo.py from bundled scripts directory (Not for general …
    0
    schroedinger
  20. Go to item
    Node / Sink
    Canvas Fingerprint Writer
    Schrödinger I/O
    Write Canvas Binary Fingerprint to File
    0
    schroedinger

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