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Domain - Leverage

Enalos Nodes for KNIME version 1.0.100.qualifier by NovaMechanics Ltd (www.novamechanics.com)

Applicability Domain (APD) based on the extent of extrapolation.

Domain of model applicability must be defined to flag compounds in the test set for which predictions may be unreliable. In this node extent of extrapolation method is used to define the domain of applicability of the model that could be used for screening new compounds. Predictions for only those compounds that fall into this domain may be considered reliable.

Extent of extrapolation is one simple approach to define the applicability of the domain [A. Tropsha, P. Gramatica, V.K. Gombar, QSAR Comb. Sci. 22 (2003) 69-77 and A. Golbraikh, A. Tropsha, J. Mol. Graph. Model. 20 (2002) 269-276]. It is based on the calculation of the leverage hi for each chemical, where the in silico model is used to predict its activity property:

hi = χi^T(X^TX)χi

The descriptor-row vector of the query compound and X is the k x n matrix containing the k descriptor values for each one of the n training compounds. A leverage value greater than 3k/n is considered large. It means that the predicted response is the result of a substantial extrapolation of the model and may not be reliable.

More details and examples can be found here: www.novamechanics.com/knime.php

If this node is useful to you, please cite the following papers:

G. Melagraki, Α. Afantitis, H. Sarimveis, P.A. Koutentis, O. Igglessi – Markopoulou and G. Kollias "Predictive QSAR workflow for the in silico identification and screening of novel HDAC inhibitors" Molecular Diversity 13 (3), pp. 301-311.

Α. Afantitis, G. Melagraki, H. Sarimveis, P.A. Koutentis, J. Markopoulos and O. Igglessi – Markopoulou "Development and Evaluation of a QSPR Model or the Prediction of Diamagnetic Susceptibility" QSAR Comb. Sci. 27, 2008, No. 4, 432 – 436.

Options

Input Ports

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Training Set (Please insert only selected attributes)
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Test or Virtual Screening Set (Please insert the same attributes with Training Set)

Output Ports

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Leverage for each compound of the Test/ Virtual Screening Set, Leverage Limit for the Training Set, Result: Reliable / Unreliable

Views

Results
Each Enalos Domain of Applicability node provides a summary View with information about the percentage of the reliable and the unreliable predictions.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.3

A zipped version of the software site can be downloaded here.

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