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Prime Side Chain Sampling

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

Options

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

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

Parameter flow variables

Flow variable prefix keyword: PrimeSideChainInput
Use this prefix to control the keywords in the input file (.inp). If a match is found for the keyword, the existing value in the .inp file will be updated with the value specified in flowvariable. If a match is not found, then a new entry will be added. To remove an existing keyword, use the value "_rm_"
For example,
Flow variable name: PrimeSideChainInput-PRIME_TYPE
Flow variable value: MC

Input Ports

: Input data table containing molecules in Maestro format

Output Ports

: Output data table containing refined molecules in Maestro format

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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:

v5.2

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

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: 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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