Compare Experimental Affinity with End Point Analysis Results [Utility]
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
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
Titles of required parameters (promoted names)
Output Dataset (data_out) type: dataset_out: Output dataset of successful calculationsDefault: Output for Compare Experimental Affinity with End Point Analysis Results [Utility] 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]
Optional parameters (promoted names)
MD Analysis Dataset Reader (data_in) type: data_source: The Dataset produced by MD Analysis Floe Ligand Experimental Results (lig_exp_file) type: file_in: Ligand Experimental Results