Page Index - k-ngo/CATMD GitHub Wiki
52 page(s) in this GitHub Wiki:
- Home
- ⭐ Simulation Utilities
- ⭐ General Conformational & Structural Dynamics
- ⭐ Binding Pocket & Interface Analysis
- ⭐ Membrane Protein-Specific Analysis
- ⭐ Protein Interaction Mapping & Kinetics
- ⭐ Advanced Conformational & Kinetic Modeling
- Analyze and Visualize Interaction Pair Co‐occurrence
- Analyze Ion Channel Selectivity Filter Conformation
- Analyze Pairwise Electrostatic Interactions
- Calculate Energy Barriers for Ion Conduction
- Correlate Motions Between Residue Pairs (with DCCM)
- Detect Allosteric Coupling via Time‐Lagged Cross Correlation (TLCC)
- Extract Pairwise Interaction from Trajectory
- Getting Started
- Heatmap of Interaction Persistence (% of Sim. Time)
- Helix Orientation and Displacement Analysis
- Identify Key Residues Driving Ligand Association
- Identify Major Interaction Events or Conformational Deviations
- Identify Prevalent Structural States
- Interface Area & Buried Surface Area (BSA)
- Ligand & Binding Pocket Analysis
- Lipid Dwell Time Near Protein
- Local Packing Density Around Residues
- Markov State Model (MSM)
- Membrane Bending and Deformation Mapping
- Membrane Thickness & Protein Contact Remodeling
- Plot Chi Dihedral Angles
- Plot Free Energy Landscape (FEL) for Binding
- Plot Interaction Energies
- Plot Interaction Formation and Loss Distributions
- Plot Ion and Water Occupancy in Selectivity Filter
- Plot Ion Conduction Through a Channel
- Plot Phi Psi Dihedral Angles
- Plot Radius of Gyration (Rg)
- Plot Residue Mobility (B‐Factor equivalent)
- Plot RMSD (Root Mean Square Deviation)
- Plot RMSF (Root Mean Square Fluctuation)
- Plot SASA (Solvent Accessible Surface Area)
- Plot Secondary Structure Evolution
- Protein‐Lipid Contact Time Series
- Quantify Hydrogen Bond Salt Bridge Lifetime & Kinetics
- Reaction Coordinate Optimization (with TICA)
- Relabel Residue Numbers or Segment IDs
- Selection Language Tutorial
- Simulation Stability & Clashes Report
- Solvent Shell Occupancy Analysis
- Summarize and Visualize Interaction Types
- Time Series Maps of Pairwise Interactions
- Time‐Resolved Principal Component Analysis (PCA)
- Track Distance Between Groups
- Wrap and Center MD System