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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™, Flare™ and XedTools™ are detailed below.

Download all Cresset KNIME workflows

Spark workflows

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

Scaffold hopping and R-group replacement experiments can be performed using the Spark Database Search node. 

  • 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 with the Generate Spark Database node.

  • Generate a Spark database
  • Generate a Spark reagent database

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.

Cresset's patented ligand alignment method can be used with the Flare Align node to align and score molecules to a 3D reference molecule using electrostatics and shape or common substructure. 

  • Align molecules using Flare Align

Quantitative and qualitative 3D models of activity using Field QSAR models, kNN models and Activity Atlas™ can be built with the Flare Build nodes, using the Flare Score nodes to predict the activities or novelty of new molecules. The Flare Field Descriptors node can be used to create a matrix of Cresset 3D descriptors, modeling the electrostatic and shape properties of aligned models, to use with KNIME machine learning models.

  • Create a Field QSAR model using Flare Build Field QSAR
  • Calculate predicted activities for molecules against a Field QSAR model using Flare Score Field QSAR
  • Create a k Nearest Neighbor (kNN) model using Flare Build kNN
  • Calculate predicted activity for molecules against a kNN model using Flare Score kNN
  • Create an Activity Atlas model using Flare Build Activity Atlas
  • Calculate Novelty for molecules against an Activity Atlas model using Flare Score Activity Atlas
  • Calculate Cresset 3D descriptors and use them to build a regression model
  • Generate a matrix of 3D field descriptors for aligned ligands

The Flare Docking node runs docking and scoring experiments using the Lead Finder™ docking algorithm, now fully integrated in Flare.

  • Dock covalent ligands with Flare Docking
  • Dock ligands with Flare Docking
  • Template dock ligands with Flare Docking
  • Dock ligands and calculate Electrostatic Complementarity™ using pyflare

The pyflare node enables access to all Flare functionalities, including protein preparation and Electrostatic Complementarity, through the Python API.

  • 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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