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

Best Friends (Incoming)

• Molecule Reader (to MAE) (24 %) 
• Concatenate (16 %) Streamable
• Get PDB (11 %) 
• Desmond Trajectory Extract Frames (11 %) 
• SDF Reader (8 %) 
• Show all 14 recommendations

Best Friends (Outgoing)

• Run Maestro (34 %) 
• Protein Preparation Wizard (17 %) 
• Molecule Writer (from MAE) (10 %) 
• Row Splitter (10 %) Streamable
• Table Viewer (7 %) 
• Show all 10 recommendations

Workflows

• Binding site shape clustering (KNIME Hub) 
• Binding site shape clustering (KNIME Hub) 
• Binding site shape clustering (Schrödinger) 
• Dock in most similar binding site (KNIME Hub) 
• Docking in the most similar binding site (KNIME Hub) 
• Show all 43 workflows

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.