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Prime Side Chain Sampling

Schrödinger extension for KNIME Workbench version by Schrödinger

This node runs protein structure refinement by prediction side chains using the Protein Local Optimization Program (PLOP). The residues of the input structure, to carry out side chain prediction, are generated using the input ASL expression.

Backend implementation

scripts/ScriptCenter/asl_to_residue.py converts the ASL expression to residues
$SCHRODINGER/prime predicts the side chains at the specified residues


Output Column Structure
Choose the output columns:

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

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

Output only - Only Output structures

Include Log in output
Include the log in the output data table for each structure
ASL expression used to generate the residues for side chain sampling
ASL from selected column
Use selected column from input table containing ASL expressions for each structure

Input Ports

Input data table containing molecules in Maestro format

Output Ports

Output data table containing refined molecules in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)



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