SZYBKI - Ligand Minimization in a Rigid Active Site

SZYBKI - Ligand Minimization in a Rigid Active Site is a tool for optimizing ligands in a fixed protein active site. Only the ligand is modified, while the protein is kept fixed during the optimization.

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

Extra Required Parameters

• Input Protein (data_source) : Dataset containing Protein or DU
• Input Ligands (data_source) : Dataset containing molecules to minimize
• Output Dataset (dataset_out) : Output dataset of successful calculations

  Default: Output for SZYBKI - Ligand Minimization in a Rigid Active Site
• Add interaction hints (boolean) : Option add interactions to the design units.

  Default: False
• Build C-terminal caps (boolean) : Option to cap broken C-termini in protein chains.

  Default: False
• Build missing loops (boolean) : Option to build missing loops (if information is available to do so)

  Default: False
• Build N-terminal caps (boolean) : Option to cap broken N-termini in protein chains.

  Default: False
• Build partial sidechains (boolean) : Option to build missing or partial protein sidechains.

  Default: False
• Assign charges and radii (boolean) : Option to assign partial charge and radii. Charges cannot be assignedif there are missing hydrogen atoms. In thise case protonate will need to be enabled.

  Default: False
• Fix backbone atom issues (boolean) : Option to fix backbone atom issues in protein chains.

  Default: False
• Optimize Existing Protons (boolean) : Option to re-optimize hydrogens already assigned.

  Default: False
• Protonate (boolean) : Option to add and optimize protons in the system.

  Default: False
• Strict protonation mode (boolean) : Option to fail prep if protons could not be added.

  Default: False
• Failed Dataset (dataset_out) : Output dataset of failed calculations

  Default: Failed Output for SZYBKI - Ligand Minimization in a Rigid Active Site