Molecular Surface Area

There are two types of available molecular surface area calculations, van der Waals (vdW) and solvent accessible (SA). The calculation method is based on Ferrara et al.

Options

Surface area
  • Van der Waals: calculates the van der Waals surface of the molecule (in Å2).
  • Solvent Accessible: calculates the solvent accessible surface of the molecule (in Å2).
Solvent radius
Sets the radius of the solvent molecule (by default water, 1.4 Å).
Show surface area increments
If set, atomic increments are shown.
Take major microspecies at pH
The surface area of the major microspecies present at the given pH is calculated.
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 molecular surface area.

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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:

v5.2

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v240101
On NodePit since: 2023-12-06
Last update: 2024-04-23
Tags: Streamable
KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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