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Cresset KNIME example workflows

Cresset software solutions can be accessed through KNIME nodes that call the corresponding command line application behind the scenes. Example workflows that encompass each of the Cresset KNIME nodes are available to download, and workflows for Spark™, Forge™, Flare™ and XedTools™ are detailed below.

Download all Cresset KNIME workflows

Spark workflows

Our scaffold hopping and R-group replacement tool, Spark, enables you to generate highly innovative ideas for your project to explore chemical space and escape IP and toxicity traps. 

  • R-group replacement using docking in Spark
  • R-group replacement using Spark
  • Replace a section of a molecule using Spark

Spark fragment and reagent databases are derived from commercially-available compounds and reagents, literature reports and theoretical studies. You can also create custom databases of replacement moieties using the database generator functionality.

  • Generate a Spark database
  • Generate a Spark reagent database

Forge workflows

Note: Forge is Cresset's legacy ligand-based workbench providing an informative approach to molecule design and structure activity relationship (SAR) analysis.

Use Cresset's patented ligand alignment method to align and score molecules to a 3D reference molecule using electrostatics and shape or common substructure. 

  • Align molecules using Forge Align

FieldTemplater™ allows you to compare molecules using their electrostatics, shape and hydrophobic fields in order to find common patterns.

  • Create a Pharmacophore using FieldTemplater

Activity Miner™ is a tool for generating similarity, distance or disparity matrices from a set of aligned molecules, using 2D and 3D measures of similarity.

  • Clustering in 3D using Activity Miner
  • View disparity matrix and hierarchical clustering in 3D using Activity Miner
  • Viewing the disparity matrix using Activity Miner

Quantitative and qualitative 3D models of activity using Field QSAR, Machine Learning models and Activity Atlas™ can be built with the Forge Build node, then using the Forge Score node to predict the activities or novelty of new molecules.

  • Create a Field QSAR model using Forge Build
  • Calculate predicted activities for molecules against a 3D QSAR model using Forge Score
  • Create a kNN model using Forge Build
  • Calculate predicted activity for molecules against a kNN model using Forge Score
  • Create a Machine Learning classification model and calculate predicted activity
  • Create a Machine Learning regression model and calculate predicted activity
  • Create an Activity Atlas model using Forge Build
  • Calculate Novelty for molecules against an Activity Atlas model using Forge Score

Flare workflows

Flare is an agile ligand-based and structure-based drug design solution enabling research chemists to discover novel small molecules more efficiently and effectively in a single platform. pyflare enables access to all Flare functionalities, including protein preparation, docking and Electrostatic Complementarity™, through the Python API.

Example worflows available using Flare methods:

  • Dock ligands and calculate Electrostatic Complementarity using pyflare
  • Prepare proteins using pyflare

XedTools workflows

XedTools provides access to access to core technologies such as ligand minimization and conformation generation using Cresset's proprietary XED force field.

  • Generate conformations for a set of molecules using XedeX
  • Minimize a set of molecules inside a protein using XedMin

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