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