Cryptic Pocket Detection Floes

Documentation for Cryptic Pocket Detection Floes package.

Contents:

• Tutorials
  • Creating an Orion Project (Optional)
  • Design Unit Preparation for Beta-Lactamase (Optional)
  • Cryptic Pocket Detection Tutorial: Exposons Analysis of Beta-lactamase (single-solvent)
  • Cryptic Pocket Detection Tutorial: Exposons Analysis of Beta-lactamase (mixed-solvent)
  • Cryptic Pocket Detection Tutorial: Cosolvent Binding Free Energy Analysis of Beta-lactamase (mixed-solvent)
  • Cryptic Pocket Detection Tutorial: Cooperative Cosolvent Binding Analysis of Beta-Lactamase (mixed-solvent)
• OpenEye Cryptic Pocket Detection Floes - Documentation
  • A1. Protein Sampling (for Cryptic Pockets): Solvate and Equilibrate Target Protein
  • A2. Protein Sampling (for Cryptic Pockets): Calculate Normal Modes
  • A3a. Protein Sampling (for Cryptic Pockets): Run a Weighted Ensemble MD Simulation
  • A3b. Protein Sampling (for Cryptic Pockets): Continue a Weighted Ensemble MD Simulation
  • A4. Protein Sampling (for Cryptic Pockets): Check for Protein Denaturation
  • B1. Trajectory Analysis (for Cryptic Pockets): Per-Residue SASA
  • B1. Trajectory Analysis (for Cryptic Pockets): Residue-Cosolvent Distances
  • B2. Trajectory Analysis (for Cryptic Pockets): Cluster Conformations
  • C1. Cryptic Pocket Detection: Cooperative Cosolvent Binding Analysis
  • C1. Cryptic Pocket Detection: Cosolvent Binding Free Energy Analysis
  • C1. Cryptic Pocket Detection: Exposon Analysis
  • C2. Cryptic Pocket Detection: Receptor Creation
• Release Notes
  • 0.1.0 July 2023
• Bibliography