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 one or two receptors for each pocket identified using probe occupancy analysis. The dataset can be visualized on the 3D & 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)

Medoids Structures (medoids_dus): A dataset containing medoids structures.

  • Required

  • Type: dataset_out

  • Default: Medoids Structures (Probe Occupancy Analysis)

Superposed Holo Design Units (holo_data_out): Superposed holo design units dataset to be used for validation. The superposed design units of holo structures can be compared with the pocket receptor design units to check the overlap between the ligand in the holo structure and the pocket receptors.

  • Type: dataset_out

  • Default: Superposed holo design units

Cryptic Pocket Analysis Advanced Settings

Important Residues (c2_select_string_key_resids): String for selecting functionally important residues such as 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

Minimum Ligandability Score (c2_lig_score_cutoff): Lower bound on the normalized ligandability score of pockets that are sent to the output dataset.

  • Type: decimal

  • Default: 0.05

Holo Design Units (Optional) (holo_data_in): Holo design units to be used for validation. These design units will be superposed with the pocket receptor design units.

  • Type: data_source

Selection Range for Trajectories

Start Iteration (b1_start_iteration): The start iteration of WE segments to be extracted. Leave empty to extract from the first iteration that is available.

  • Type: integer

End Iteration (b1_end_iteration): The end iteration of WE segments to be extracted. Leave empty to stop extracting at the last iteration that is available.

  • Type: integer