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