FreeForm - Bound Ligand Configurational Free Energies with SZYBKIΒΆ

FreeForm - Bound Ligand Configurational Free Energies with SZYBKI is a tool for evaluating the free energy associated with selecting a particular conformer (or a set of conformers) out of the whole conformational ensemble in solution, as well as the additional energy required to restrain to the particular conformation in the bound state.

The minimal input into FreeForm Restriction Energies is a dataset of molecules in 3D format.

Output from the FreeForm Restriction Energies floe consists of two datasets. The first results dataset mimics that of the FreeForm Conformer Energies containing a conformational ensemble per input molecule, along with the associated free energies, and the probability of states for each conformer. The second dataset provides information regarding the total and global restriction energies associated with each input conformer. The unit of free energy is kcal/mol.

Extra Required Parameters

  • XY plot Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Plot
  • Table Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Table
  • Database Molecules (data_source) : Dataset containing one or more molecules
  • Failed Dataset (dataset_out) : Output dataset of failed calculations
    Default: Failed Output for FreeForm - Bound Ligand Configurational Free Energies with SZYBKI
  • Delete Field (string) : The field on the input record to be deleted.
  • XY plot Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Plot
  • Table Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Table
  • Delete Field (string) : The field on the input record to be deleted.
  • XY plot Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Plot
  • Table Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Table
  • Threshold (integer) : Counter above which port should be switched
    Default: 8 Min: 1
  • Output Dataset (dataset_out) : Output dataset of successful calculations
    Default: Output for FreeForm - Bound Ligand Configurational Free Energies with SZYBKI
  • XY plot Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Plot
  • Table Image (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: Table
  • Output Ensemble (dataset_out) : Output of Freeform ensemble
    Default: Freeform Ensemble