C2. Cryptic Pocket Detection: Receptor Creation

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 creates design units with receptors constructed from site residues defined for a user specified cryptic pocket and calculates the receptor volume.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Solvated and Equilibrated Design Unit (du_data_in): This is the ‘Solvated and Equilibrated Design Unit’ output dataset from the ‘A1. Protein Sampling (for Cryptic Pockets): Solvate and Equilibrate Target Protein’ floe.

  • Required

  • Type: data_source

MSM Weighted Medoids (conf_data_in): This is a ‘MSM Weighted Medoids’ dataset generated by one of the ‘C1. Cryptic Pocket Detection’ Floes: ‘Cooperative Cosolvent Binding Analysis’, ‘Cosolvent Binding Free Energy Analysis’, or ‘Exposon Analysis’.

  • Required

  • Type: data_source

Ranked Pockets (pocket_data_in): This is a ‘Ranked Pockets’ dataset generated by one of the ‘C1. Cryptic Pocket Detection’ Floes: ‘Cooperative Cosolvent Binding Analysis’, ‘Cosolvent Binding Free Energy Analysis’, or ‘Exposon Analysis’.

  • Required

  • Type: data_source

Pocket Rank ID (pocket_rank): The rank ID number for the pocket of interest. The pocket and its rank ID can be selected by analyzing an ‘interactive network plot of pockets’ in the Floe report generated by one of the ‘C1. Cryptic Pocket Detection’ Floes: ‘Cooperative Cosolvent Binding Analysis’, ‘Cosolvent Binding Free Energy Analysis’, or ‘Exposon Analysis’.

  • Required

  • Type: integer

Outputs

Output Dataset (success_data_out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Cryptic Pocket Receptors Dataset

Failure Output Dataset (failure_data_out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Cryptic Pocket Receptors - Failure

Floe Report Output Collection (floe_report_name): File name for the output floe report.

  • Required

  • Type: string

  • Default: Pocket Receptor Volume Floe Report

Advanced Options

Minimum Receptor Volume (volume_min): An lower bound on the receptor volumes of design units that are sent to the output dataset.

  • Type: decimal

Maximum Receptor Volume (volume_max): An upper bound on the receptor volumes of design units that are sent to the output dataset.

  • Type: decimal