IconForge Score k Nearest Neighbour (kNN)0 ×

Cresset KNIME Nodes version 2.1.0.20539 by www.cresset-group.com

Calculates predicted activity for molecules using a k-nearest neighbor (kNN) model generated with Forge or the 'Forge Build k Nearest Neighbour (kNN)' node. If the model was created using the Cresset field/shape similarity method then molecules must be pre-aligned in a manner consistent with the original model to make sensible predictions- the falign program or the 'Forge Align' node are ideal for this.

Please refer to the Forge manual for a detailed description of the science behind Field QSAR models in Forge and the corresponding model building options.

This node wraps the Forge Score executable 'fscore', which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the "Cresset Home" preference or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the "fscore Path" preference or the CRESSET_FORGESCORE_EXE environment variable to point directly at the executable itself.

The Forge Score k Nearest Neighbour (kNN) node can be configured to use additional resources to perform calculations. The time taken for the node to run will be drastically reduced using the Cresset's Engine Broker. To use this facility either set the "Cresset Engine Broker" preference or the CRESSET_BROKER environment variable to point to the location of your local Engine Broker. If you do not currently have the Cresset Engine Broker then contact Cresset (enquiries@cresset-group.com) for pricing on local and cloud based brokers.

For more information visit www.cresset-group.com or contact us at support@cresset-group.com.

Options

Basic

Structure Column
The molecules in the prediction set to fit to the kNN model. The molecules must be pre-aligned if using the Cresset field/shape similarity method.
Assign formal charges to moving molecules
If checked, protonation states for the input molecules are set using Cresset's charging rules. Acids will be deprotonated, primary amines protonated, etc.
Automatic calculate number of neighbors to consider
If checked, then the optimal number of components as determined by Forge or the ‘Forge Build k Nearest Neighbour (kNN)’ node will be used.
Number of neighbors to consider when fitting compounds to the model
Manually sets the number of neighbors k to use when fitting compounds to the model. The q^2 information for this setting can be viewed by using a Forge Project Viewer node or by using the Forge Model Info node on the Forge project containing the model.

Input Ports

The molecules in the prediction set to fit to the kNN model. The molecules must be pre-aligned if the model uses Cresset field similarity as the metric.
A Forge project containing the k-nearest neighbor (kNN) model. The 'Forge Build k Nearest Neighbour (kNN)' node or the fbuild program are ideal for creating the Forge project.

Output Ports

The input molecules with their predicted activity, 'distance to model' and ‘activity error’ information.

Workflows

Update Site

To use this node in KNIME, install Cresset KNIME Nodes from the following update site:

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