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


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)


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


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)