A4. Protein Sampling (for Cryptic Pockets): Check for Protein Denaturation¶
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
This floe performs analysis to evaluate structural integrity of conformations sampled by Weighted Ensemble simulations. The analysis includes calculation of fraction of native contacts and RMSD of conformational snapshots with respect to the initial conformation. Fraction of native contacts or RMSD values are then mapped onto the progress coordinates grid.
Promoted Parameters
Title in user interface (promoted name)
Inputs
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 MD simulation trajectories.
Type: integer
Default: 1
End Iteration (end_iteration): Iteration number for ending analysis of Weighted Ensemble MD 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
Parameters for Free Energy Maps/Surfaces (optional)
Apply Weight (weight_option): Apply weights from WE-MD simulations when generating free energy maps.
Type: boolean
Default: True
Choices: [True, False]
Number of Histogram Bins (number_bins): Number of bins for plotting density distribution.
Type: integer
Default: 100
Maximum Free Energy Value (max_free_energy): Maximum value (in kcal/mol) for showing the 2D free energy map.
Type: decimal
Default: 50.0
Native Contact Map (is_ncfractions_on): Defines whether to plot the projection of the fraction of native contacts compared to the reference structure. The projection shows the average fraction of native contacts for all selected conformations for a given progress coordinate (pair).
Type: boolean
Default: True
Choices: [True, False]
RMSD Map (is_rmsd_on): Defines whether to plot the projection of the backbone root mean square deviation (RMSD) compared to the reference structure. The projection shows the average RMSD for all selected conformations for a given progress coordinate (pair).
Type: boolean
Default: True
Choices: [True, False]
Outputs
Analysis Report Title (analysis_report_title): Title for the analysis report.
Type: string
Default: Protein Denaturation Floe Report
Output Dataset (data_out): Output dataset for the analysis results with one record per MD segment.
Required
Type: dataset_out
Default: Protein Denaturation Check Output