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Align Binding Sites

This script performs a pairwise superposition of multiple structures using the C-alpha atoms of selected residues. The reference structure for the alignment is the first structure in the input Maestro (.mae) file. The C-alpha atoms for the alignment are from residues within the specified cutoff distance from the ligand in the reference structure. Alternatively, a list of residues may be given for the alignment, which must correspond to residues in the reference structure. C-alpha atoms in the mobile structure greater than the specified distance from any C-alpha in the reference are not considered in the alignment.

Backend implementation

utilities/align_binding_sites
The script align_binding_sites is used to implement this node.

Options

Column containing input structures

Select column in the data input table containing the structures

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Active site cutoff distance

Binding site cutoff distance from the ligand in Angstrom

Distance to consider matching atoms

Atom pairs greater than this distance are not considered in the alignment

Residues for the alignment

Residues for the alignment. This option overrides the use of -c/-cutoff. Format for a residue is chain:resnum. If their is no chain name, use "_". For example, A:123,A:456,_:999 for residue numbers 123 and 456 from chain A and residue number 999 from a blank chain. At least three residues are required. The comma-separated list should not have spaces.

Structures are pre-aligned

Structures are pre-aligned. Protein Structure Alignment (SKA) is not run if this option is selected.

Input Ports

: Structures in Maestro or Pdb format

Output Ports

: Aligned structures in Maestro or Pdb format
: RMSD data for structures

Views

Std output/error of Align Active Sites: Std output/error of Align Active Sites

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.7

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

Plugin provider: Schrödinger

Plugin version: 25.2.133.v202505021925

On NodePit since: 2025-12-25

Last update: 2026-01-08

KNIME versions: v5.7, v5.6, v5.5, v5.4, 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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