MATLAB Workflow for MD Analysis: From Raw Signal Extraction (Center of Mass/Dipole) to Core Residue Identification via ACF Fitting

This repository provides a comprehensive MATLAB-based analytical framework for processing Molecular Dynamics (MD) trajectories. The workflow covers the entire pipeline, starting from raw signal extraction to the statistical identification of structural-dynamical hotspots (Core Residues). Key Features: 1. Signal Processing: Extracts raw Center of Mass (CoM) and Dipole moment information from MD trajectories. 2. Metric Calculation: Computes proximity ($u$) and alignment ($m$) metrics to quantify residue-target interactions. 3. Dynamic Analysis: Calculates Autocorrelation Functions (ACF) for each metric to observe time-dependent decay. 4. Adaptive Fitting: Employs a bi-exponential fitting protocol to extract fast and slow relaxation times ($\tau_{f}, \tau_{s}$). File Structure: Data Files (.mat): 4 initial files containing raw trajectory signals (Center of Mass and Dipole coordinates). Source Code (.m): upload_01_Data.m: Processes raw signals to calculate $u, m$ metrics and generates the corresponding ACFs. upload_02_ACF_Fitting.m: Performs the dual-metric adaptive fitting and to find final hotspots. How to Use: Place all .mat files and .m scripts in the same MATLAB working directory. Execute upload_01_Data.m: first to generate the metric-based dataset. Execute upload_02_ACF_Fitting.m to perform the dynamic analysis.