New KNIME node and Pipeline Pilot (V2.4.0) components released

We are delighted to announce the release of the latest set of workflow components for KNIME™ and Pipeline Pilot™ environments. This release introduces nodes for Activity Atlas, a component of Forge, and kNN plus a number of enhancements to existing components.

New example workflows and protocols have been created for both KNIME and Pipeline Pilot to illustrate the usage of these new components.

Activity Atlas

The release of Forge 10.4 introduced Activity Atlas – a new qualitative model for SAR interpretation and communication which has proved popular with both medicinal and computational chemists. Activity Atlas summarizes the SAR for a series into a visual 3D model that can be used to inform new molecule design. It is particularly useful for those project teams where there is not enough SAR for a traditional 3D-QSAR approach.

Activity Atlas calculates and displays as 3D visualizations:

  • ‘Activity cliff summary’: what do the activity cliffs tell us about the SAR?
  • ‘Average of actives’: what do active molecules have in common?
  • ‘Regions explored’: where have I been? For a new molecule, would making it increase our understanding? This analysis also calculates a novelty score for each molecule.

The new Activity Atlas models are created using Cresset’s Forge Build node and can be used with the Forge Score node to provide a novelty score for new compound and library designs.

In this release of our workflow solutions we are delighted to support the creation and use of Activity Atlas models. An example workflow for KNIME is shown below.

Create an Activity Atlas model in KNIME
Create an Activity Atlas model in KNIME

k-Nearest Neighbor (k-NN) Models

k-Nearest Neighbor (k-NN) models of activity are popular and robust ways of predicting the activity of new molecule designs. We have introduced this approach with the traditional 2D circular fingerprint method of measuring similarity but have added the ability to use 3D similarity as well. This innovation enables the building of models using any combination of Field similarity and Gaussian shape similarity.

The kNN models are created with Forge Build nodes and can be deployed using the Forge Score node to score new molecules.

An example protocol for Pipeline Pilot is shown below.

Create a kNN model in Pipeline Pilot
Create a kNN model in Pipeline Pilot

These new and improved components simplify the integration of Cresset’s advanced technology into the automation environments of KNIME and Pipeline Pilot, allowing you to gain knowledge and direction for your drug discovery projects within a familiar interface.

Cresset customers can contact support to get these new components free of charge. If you would like to try the software yourself you can download a free evaluation.

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