CATMD is a web tool for analyzing molecular dynamics simulation data. It integrates a range of tools to process trajectories, evaluate structural properties, and study molecular interactions. The toolkit is organized into different sections covering the full spectrum of MD analysis needs, catering to users across experience levels in computational biophysics.

⭐ Simulation Utilities

Tools	Use This For...
Wrap and Center MD System	Correcting periodic boundary artifacts and aligning trajectories for analysis
Simulation Stability & Clashes Report	Verifying simulation integrity and detecting steric issues or instabilities
Relabel Residue Numbers or Segment IDs	Renumber residues or reassign segment IDs to specific atom selections

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⭐ General Conformational & Structural Dynamics

Tools	Use This For...
Plot RMSD (Root Mean Square Deviation)	Monitoring overall structural deviation during the simulation
Plot RMSF (Root Mean Square Fluctuation)	Identifying flexible vs. rigid regions across the trajectory
Plot SASA (Solvent Accessible Surface Area)	Measuring exposure of residues to solvent over time
Track Distance Between Groups	Monitoring distance changes between two atoms or groups
Plot Phi/Psi Dihedral Angles	Analyzing protein backbone conformations
Plot Chi Dihedral Angles	Assessing sidechain rotamer changes over time
Plot Radius of Gyration (Rg)	Estimating overall protein compactness or unfolding
Plot Residue Mobility (B-Factor equivalent)	Visualizing residue fluctuation as thermal mobility proxy
Helix Orientation and Displacement Analysis	Tracking helix tilting or positional shifts
Identify Major Interaction Events or Conformational Deviations	Detecting transitions or key interactions during dynamics
Plot Secondary Structure Evolution	Following changes in helices, sheets, and loops over time
Correlate Motions Between Residue Pairs (DCCM)	Identifying correlation in residue motions
Detect Allosteric Coupling (TLCC)	Identifying potential allosteric communication
Identify Prevalent Structural States	Clustering dominant conformational states

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⭐ Binding Pocket & Interface Analysis

Tools	Use This For...
Analyze Pairwise Electrostatic Interactions	Detecting favorable or repulsive electrostatic contributions in binding regions
Local Packing Density Around Residues	Finding tightly or loosely packed regions in the protein structure
Interface Area & Buried Surface Area (BSA)	Measuring how much surface gets buried when ligand binds to the receptor
Solvent Shell Occupancy Analysis	Monitoring hydration shell stability around a specific position
Plot Interaction Energies	Estimating interaction strength between molecules or domains
Ligand & Binding Pocket Analysis	Tracking structural and spatial changes in the ligand and its binding pocket
Plot Free Energy Landscape (FEL) for Binding	Visualizing conformational or binding energy basins

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⭐ Membrane Protein-Specific Analysis

Tools	Use This For...
Plot Ion Conduction Through a Channel	Tracking ions as they pass through membrane channels
Plot Ion and Water Occupancy in Selectivity Filter	Analyzing ion/water positioning within the channel pore
Calculate Energy Barriers for Ion Conduction	Estimating energy cost for ion movement through membrane channels
Analyze Ion Channel Selectivity Filter Conformation	Quantifying selectivity filter geometry and flexibility over time
Membrane Thickness & Protein Contact Remodeling	Assessing membrane deformation and lipid contact dynamics
Membrane Bending and Deformation Mapping	Quantifying and visualizing membrane curvature, leaflet deformation, and protein-induced bilayer remodeling
Protein-Lipid Contact Time Series	Tracking changes in lipid-protein interaction over time
Lipid Dwell Time Near Protein	Measuring how long lipids stay near specific protein surfaces

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⭐ Protein Interaction Mapping & Kinetics

Tools	Use This For...
Extract Pairwise Interaction from Trajectory	Extracting all molecular interactions from trajectory
Time Series Maps of Pairwise Interactions	Viewing changes in specific residue-residue interactions over time
Heatmap of Interaction Persistence (% of Sim. Time)	Identifying stable vs. transient interactions
Summarize and Visualize Interaction Types	Visualizing both the global prevalence of contact types and the residue-level details
Quantify Hydrogen Bond Lifetime & Kinetics	Measuring how long hydrogen bonds persist and how often they form/break
Quantify Salt Bridge Lifetime & Kinetics	Measuring how long salt bridges persist and how often they form/break
Plot Interaction Formation and Loss Distributions	Determining when interactions appear or disappear
Analyze and Visualize Interaction Pair Co-occurrence	Detecting interaction pairs that occur together more/less often than expected
Identify Key Residues Driving Ligand Association	Pinpointing residues most critical for ligand binding

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⭐ Advanced Conformational & Kinetic Modeling

Tools	Use This For...
Reaction Coordinate Optimization (with TICA)	Extracting slowest collective motions to define reaction pathways
Time-Resolved Principal Component Analysis (PCA)	Identify dominant modes of motion within a selected group of atoms
Markov State Model (MSM)	Modeling timescale and kinetics of conformational transitions

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