Software

Cresset KNIME™ integration

Cresset solutions are available through easy to use graphical user interfaces, command lines and through workflow solutions such as KNIME™ and Pipeline Pilot™. Using the KNIME interface enables integration of our approach into standard workflows and with other applications. We provide access to all our applications through KNIME nodes that call the corresponding command line application behind the scenes.

Forge nodes

Forge is a powerful computational chemistry suite for understanding structure activity relationship (SAR) and design.

In KNIME the Forge nodes enable ligand comparisons and investigation, building of qualitative and quantitative 3D models of activity, scoring of new molecule designs, creation of molecular similarity and disparity matrices, building of detailed pharmacophores.

  • Forge Align : Align and score molecules to a 3D reference molecule using electrostatics and shape or common substructure. Molecules are conformationally hunted if necessary
  • FieldTemplater™: Compare molecules using their electrostatics, shape and hydrophobic fields in order to find common pharmacophores
  • Activity Miner™: Generate similarity, distance or disparity matrices from a set of aligned molecules, using 2D and 3D measures of similarity
  • Forge Build/Score Field QSAR: Generate 3D-QSAR models, and predict activities for new molecules using a Forge 3D-QSAR model
  • Forge Build/Score Machine Learning: Generate Machine Learning (kNN, Random Forest, RVM and SVM) regression or classification models, and predict activities for new molecules using a Forge Machine Learning model
  • Forge Build/Score Activity Atlas: Generate qualitative Activity Atlas™ models, and predict the novelty of new molecules using an Activity Atlas model
  • Forge Molecule Viewer: Launch Forge to view the electrostatic fields around your molecules, or to view the results from other Cresset nodes
  • Forge Project Viewer: Launch Forge to view Forge projects

The full list of Forge nodes can be found in the release notes.

KNIME 2.5.0 workflow

Spark nodes

Spark enables you to move to new series and non-obvious IP by swapping scaffolds and exploring accessible R-groups. Given a ‘starter molecule’, you can select a section to replace and Spark will suggest a list of new molecules containing replacement moieties with similar electrostatic and steric properties. Spark comes with several databases of moieties generated from fragmentation of commercially-available compounds, active molecules reported in the literature and available reagents. In addition you are able to generate your own databases of replacement moieties using the database generator functionality.

In KNIME the Spark nodes provide access to the scaffold hopping and R-group exploring capabilities with a specialized node to enable graphical specification of the portion of the starter molecule to be replaced. Lastly a database creation node is included.

  • Spark Database Search – search databases for novel scaffolds or R-groups for a specified molecule
  • Spark Fragment Selector – enables the graphical selection of the region to be replaced by Spark in a database search experiment
  • Generate Spark Database – generate or updating spark databases of fragments or reagents

Flare™ nodes

Flare is a structure-based design tool for the visualization and analysis of protein-ligand complexes. With Flare, you can gain vital knowledge of protein and ligand electrostatics to perfect new molecule design, predict activity for new molecule designs using Electrostatic Complementarity™ scoring, design new molecules and dock them to your protein target, minimize your protein-ligand complex to achieve the optimal interaction for each compound, calculate the location and stability of water molecules in your protein, use the energetics of ligand binding to guide lead optimization.

In KNIME the Flare nodes enable full access to the Flare functionality through the Flare Python API.

  • Flare Viewer: Launches Flare to view ligand and protein structures
  • pyflare: Runs a Python script which has access the Flare Python API

XedTools nodes

The XedTools nodes give access to core technologies such as ligand minimization and conformation generation.

  • XedMin – a ligand minimizer (using Cresset’s proprietary XED force field) to optimize ligands in isolation or in a specified context such as the protein active site.
  • XedeX – create low energy, diverse conformation populations for a ligand.

Viewer nodes

Cresset supplies a generic viewer node that calls the main Forge or Torch graphical user interfaces on the client machine. This node is useful for visualizing the electrostatic fields around molecule or for viewing the results of other Cresset nodes.

Licensing

The KNIME nodes require you to accept the terms of our license agreement when they are installed but do not require further license files. However, the software used by the KNIME nodes does require a valid license file. Contact us for more information.

Examples

See example workflows that encompass each of the Cresset KNIME nodes.

Try Cresset solutions on your project

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