logP

The logP Plugin calculates the octanol/water partition coefficient, which is used in QSAR analysis and rational drug design as a measure of molecular hydrophobicity. The calculation method is based on the publication of Viswanadhan et al. The logP of a molecule is composed of the increment of its atoms. However, the algorithm described in the paper was modified at several points: 1. Many atomic types were redefined to accommodate electron delocalization and contributions of ionic forms were added. 2. The logP of zwitterions are calculated from their logD value at their isoelectric point. 3. The effect of hydrogen bonds on the logP is considered if there is a chance to form a six membered ring between suitable donor and acceptor atoms. 4. New atom types were introduced especially for sulfur, carbon, nitrogen and metal atoms.

Options

Method
  • Consensus: this method uses a consensus model built on the ChemAxon and Klopman et al. models and the PhysProp database.
  • ChemAxon: this method is based on ChemAxon's own logP model, which is based on the VG method (derived from Viswanadhan et al.).
  • User defined: if a training set of structures and corresponding experimental logP values is available, it can be used as a database for logP calculations.
Training ID
If the User defined method is selected, this dropdown list becomes active. All created training sets are listed here. Choose the one to apply for the calculation.
Electrolyte concentration
  • Cl- concentration: can be set between 0.1 and 0.25 mol/L.
  • Na+ K+ concentration: can be set between 0.1 and 0.25 mol/L.
Consider tautomerization/resonance
The logP of the major tautomer will be calcutated if enabled.
Show value
Sets which logP values be displayed in the result window. It can be:
  • Increments: calculates and shows the increments for atoms one-by-one.
  • logP: shows just the value of the logP.
Structure column
The structure column.

Input Ports

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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains logP.

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.4

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v240300
On NodePit since: 2024-12-06
Last update: 2024-12-17
Tags: Streamable
KNIME versions: v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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