B1. Trajectory Analysis (for Cryptic Pockets): Residue-Cosolvent Distances¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/Molecular Dynamics
Solution-based/Virtual-screening/Target Preparation
Solution-based/Hit to Lead/Target Preparation/Enhanced Sampling
Solution-based/Target Identification/Target Preparation/Pocket Detection
Solution-based/Hit to Lead/Target Preparation/Cryptic Pocket Detection
Role-based/Computational Chemist
Task-based/Target Prep & Analysis/Pocket Detection
Description
Computes minimum distance between each protein residue and co-solvent pair for conformations sampled by Weighted Ensemble MD simulations.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Protein Sampling (Weighted Ensemble MD Simulation) Dataset (data_in): This is a ‘Protein Sampling Dataset’ output generated by ‘A3a. Protein Sampling (for Cryptic Pockets): Run a Weighted Ensemble MD Simulation’ or ‘A3b. Protein Sampling (for Cryptic Pockets): Continue a Weighted Ensemble MD Simulation’. The dataset should come from the most recent Protein Sampling job run for a given protein.
Required
Type: data_source
Selection Ranges for Trajectories
Start Iteration (start_iteration): Iteration number for starting analysis of weighted ensemble simulation trajectories.
Required
Type: integer
Default: 1
End Iteration (end_iteration): Iteration number for ending analysis of weighted ensemble simulation trajectories.
Type: integer
Stride (stride): Integer factor by which to subsample frames. (Only every stride-th frame will be read.)
Type: integer
Default: 1
Cosolvent Name (cosolvent): Residue name of the co-solvent must be identical to the one given in the topology PDB file generated.
Required
Type: string
Default: XE
Cosolvent-Residue Distance Cutoff (distance_cutoff): Cosolvent-residue distances greater than the cutoff value will be set to 0 to eliminate them from future analyses. This will allow focusing on cosolvent-protein interactions within a given distance cutoff value. (unit: Å)
Type: decimal
Default: 5.5
Outputs
Analysis Dataset (Residue-Cosolvent Distances) (data_out): This dataset stores trajectory analysis results (Residue-Cosolvent Distances) for conformations sampled in Weighted Ensemble MD simulations. Each record saves a vector of Residue-Cosolvent Distances for one trajectory segment.
Required
Type: dataset_out
Default: Trajectory Analysis (Residue-Cosolvent Distances)
Variance and Mean Dataset (Residue-Cosolvent Distances) (feature_mean_variance_out): Dataset containing variance and mean values for Residue-Cosolvent Distances.
Required
Type: dataset_out
Default: Variance and Mean (Residue-Cosolvent Distances)