ss-TEA score

Calculates ss-TEA score of sequence alignment and subfamily members.

Calculates entropies of each column/residue position in the sequence alignment. The entropy is calculated twice once for members inside the subfamily and once for members outside the subfamily. The ss-TEA score is a distance which is low when entropy within subfamily is low and entropy outside subfamily is high.
So positions with the lowest ss-TEA scores are most likely to be involved in ligand binding within the selected subfamily.

The ss-TEA can identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information.

Options

IdentifierColumn
Column to use for sequence indentifiers for sequence alignment port and subfamily port
SequenceColumn
Column to use for sequence, where the sequence is long string of amino acids

Input Ports

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Table sequence alignment with sequence identifier column and sequence column.
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Table subfamily members with sequence identifier column, subfamily must be subset of sequence alignment members of the first port.

Output Ports

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ss-TEA scores and stats

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Installation

To use this node in KNIME, install the extension 3D-e-Chem KNIME nodes 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: Netherlands eScience Center
Plugin version: 1.0.7.v202311211011
On NodePit since: 2023-12-06
Last update: 2024-12-18
KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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