SZYBKI - Ligand Minimization in a Flexible Active Site

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/SZYBKI

  • Solution-based/Small Molecule Lead-opt

  • Task-based/Ligand Posing & Analysis

  • Role-based/Computational Chemist

Description

SZYBKI - Ligand Minimization in a Flexible Active Site optimizes ligands in a flexible protein active site. The floe modifies both the ligand and the flexible part of the protein 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.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input DU/Ligand (in): Dataset containing design units or ligands to optimize. For ligand inputs, a second dataset of a Design unit must also be provided.

  • Required

  • Type: data_source

Input Design Unit (init): (Optional) Dataset containing design unit for docked ligands. An entry in this field assumes that ligands from the other dataset to be optimized against protein from this DU.

  • Type: data_source

Outputs

Output Dataset (out): Output dataset of successful calculations

  • Required

  • Type: dataset_out

  • Default: Output for SZYBKI - Ligand Minimization in a Flexible Active Site

Failed Dataset (failed): Output dataset of failed calculations.

  • Required

  • Type: dataset_out

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

SZYBKI settings

Components to keep as the ‘protein’ (protein_mask): DU components to use as the ‘protein’.

  • Type: string

  • Default: [‘protein’, ‘nucleic’, ‘cofactors’, ‘solvent’, ‘other_ligands’, ‘other_cofactors’]

  • Choices: [‘protein’, ‘nucleic’, ‘ligand’, ‘solvent’, ‘metals’, ‘counter_ions’, ‘lipids’, ‘packing_residues’, ‘sugars’, ‘undefined’, ‘cofactors’, ‘excipients’, ‘polymers’, ‘post_translational’, ‘other_proteins’, ‘other_nucleics’, ‘other_ligands’, ‘other_cofactors’]

Force Field (force_field): Built-in force field model to be used.

  • Type: string

  • Default: ff14sb_sage

  • Choices: [‘ff14sb_sage’, ‘ff14sb_parsley’, ‘mmff94’, ‘mmff94s’, ‘mmff_amber’, ‘mmffs_amber’]

Custom FF File (ff): Custom smirnoff force field file. Entry in this field creates a OEFF14SBSmirnoff force field and overrides any other force field selections

  • Type: file_in

Flexibility range (flex_range): Portion of the protein to be considered flexible, measured as the distance between initial positions of the ligand atoms and the protein atoms

  • Type: decimal

  • Default: 2.0

Solvent model (solvent_model): Solvent model to be used

  • Type: string

  • Default: Gas-phase

  • Choices: [‘Gas-phase’, ‘Sheffield’, ‘PB’]