Compare Experimental Affinity with End Point Analysis Results [Utility]

Category Paths

  • Product-based/Molecular Dynamics

  • Role-based/Computational Chemist

  • Role-based/Medicinal Chemist

  • Task-based/Molecular Dynamics

  • Task-based/Affinity Prediction

  • Solution-based/Hit to Lead/Affinity Prediction/STMD

  • Solution-based/Small Molecule Lead-opt/Affinity

Description

  • Purpose:

    • This Floe postprocesses a dataset resulting of the Protein-Ligand MD Analysis Floes to perform a comparison with a set of experimental ligand binding free energies (affinities).

  • Method Recommendations/Requirements:

    • Two inputs are required:

      • An output dataset of the Protein-Ligand MD Analysis Floes: Analyze Protein-Ligand MD, Short Trajectory MD with Analysis

      • A text file containing experimental binding free energies for at least one ligand, one experimental datapoint per line, of form “ligA_name {deltaG(exptl)} {error_deltaG(exptl)} {units}” for example, “gn1c -8.56 0.17 kcal/mol”.

  • Limitations

    • Only ligand affinities common to both experimental and calculated datasets can be compared.

  • Expertise Level:

    • Regular

  • Compute Resource:

    • Minimal

  • Keywords:

    • Utility

  • Related Floes:

    • Analyze Protein-Ligand MD

    • Short Trajectory MD with Analysis

Promoted Parameters

Title in user interface (promoted name)

  • MD Analysis Dataset Reader (in) type: data_source: The Dataset produced by MD Analysis Floe
  • Ligand Experimental Results (lig_exp_file) type: file_in: Ligand Experimental Results

Parameter title in user interface (promoted name)

  • Failed Dataset (data_out) type: dataset_out: Output dataset of failed calculations
    Default: Failed Output for Compare Experimental Affinity with End Point Analysis Results [Utility]

Parameter title in user interface (promoted name)

  • Output Dataset (data_out) type: dataset_out: Output dataset of successful calculations
    Default: Output for Compare Experimental Affinity with End Point Analysis Results [Utility]