Probe Occupancy Analysis

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

Analyzes residue-probe binding in WEMD trajectories, clusters them and performs probe occupancy analysis. In previous versions, it was run as a series of B1-C2 floes.

Promoted Parameters

Title in user interface (promoted name)

Input Data

Protein Sampling (Weighted Ensemble MD) Data (westdata_in): A ‘Protein Sampling Data’ collection generated by weighted ensemble simulations.

  • Required

  • Type: collection_source

Output Data

Pocket Receptors (pocket_receptors_dataset): A dataset containing 1 or 2 receptors for each pocket identified using probe occupancy analysis. The dataset can be visualized on the Analyze page with 3D layout

  • Required

  • Type: dataset_out

  • Default: Pocket Receptors (Probe Occupancy Analysis)

Cryptic Pocket Analysis Floe Report (floe_report_out): Floe report containing interactive network plot of cryptic pockets with structural visualization of the cryptic pockets

  • Required

  • Type: string

  • Default: Cryptic Pockets Floe Report (Probe Occupancy Analysis)

Cryptic Pocket Analysis Advanced Settings

Important Residues (c1_select_string_key_resids): String for selecting functionally important residues e.g. active site residues or a known disease mutation. Residues should be specified in <residue number><chain id> format. For example, active site consisting of residues 11, 12 (chain A) and residues 23 (chain B) should be specified as 11A, 12A, 23B (without any trailing punctuation). These residues will be displayed along with the pocket residues in the cryptic pocket floe report to visualize the location of each cryptic pocket with respect to functionally important residues.

  • Type: string

Selection Range for Trajectories

Start Iteration (b1_start_iteration): Iteration number for starting analysis of weighted ensemble simulation trajectories.

  • Required

  • Type: integer

  • Default: 1

End Iteration (b1_end_iteration): Iteration number for ending analysis of weighted ensemble simulation trajectories.

  • Type: integer