SZYBKI - Ligand Minimization in a Flexible Active SiteΒΆ

SZYBKI - Ligand Minimization in a Flexible Active Site is a tool for optimization of ligands in a flexible protein active site. Both the ligand and the flexible part of the protein are modified to perform the optimization.

The minimal input into Classic Szybki Ligand in Flexible Protein is a design unit or a 3D protein structure, and a dataset of molecules in 3D format.

Extra Required Parameters

  • Output Dataset (dataset_out) : Output dataset of successful calculations
    Default: Output for SZYBKI - Ligand Minimization in a Flexible Active Site
  • Failed Dataset (dataset_out) : Output dataset of failed calculations
    Default: Failed Output for SZYBKI - Ligand Minimization in a Flexible Active Site
  • Log Field (Field Type: String) : The field to store messages to floe report
    Default: Log Field
  • Update Component (string) : Component in DesignUnit to update.
    Default: ligand
    Choices: protein, nucleic, ligand, solvent, metals, counter_ions, lipids, packing_residues, sugars, undefined
  • Input DU/Ligand (data_source) : Dataset containing design units or ligands to optimize. For ligand inputs, a second dataset of a Design unit must also be provided.