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