B1. Trajectory Analysis (for Cryptic Pockets): Per-Residue SASA

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 per-residue solvent-accessible surface area for conformations sampled by Weighted Ensemble 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


Analysis Dataset (Per-Residue SASA) (data_out): This dataset stores trajectory analysis results (Per-Residue SASA) for conformations sampled in Weighted Ensemble MD simulations. Each record saves a vector of Per-Residue SASA for one trajectory segment.

  • Required

  • Type: dataset_out

  • Default: Trajectory Analysis (Per-Residue SASA)

Variance and Mean Dataset (Per-Residue SASA) (feature_mean_variance_out): Dataset containing variance and mean values for Per-Residue SASA.

  • Required

  • Type: dataset_out

  • Default: Variance and Mean (Per-Residue SASA)