SLC45A4 MD Analysis Pipeline

Analysis pipeline for Molecular Dynamics simulations of SLC45A4. This repository contains the essential Python and R scripts used to characterize structural stability, membrane lipid interactions, and polyamine ligand binding mechanisms (Putrescine, Spermidine, Spermine).

Repository Structure

The repository is organized as follows:

• analyze_lipids_v2.py: Main entry point for lipid interaction analysis (PyLipID).
• scripts/: Core analysis and plotting scripts.
  • Structural Analysis Plots: plot_rmsd.R, plot_rmsf.R, plot_gyrate.R, plot_sasa.R, plot_dssp_all.py
  • Membrane Analysis Plots: plot_order_params_v2.R, plot_thickness.R, plot_apl_boxplot.R, plot_density_profiles.R
  • Interactions Interactions & PCA: PCA Plots: extract_hbond_data.py, plot_hbond_starburst_dat.R, analyze_pca_projection.py, plot_pca.R
• scripts/sh/: Shell scripts used to orchestrate the analysis workflow (GROMACS wrappers).
  • run_analysis_v3.sh: Master driver script.
  • run_all_order_params.sh, run_density.sh, run_dssp_comparisons.sh, etc.

Dependencies

The analysis pipeline requires:

• Python 3.x
  • MDAnalysis
  • numpy, matplotlib, pandas
  • pylipid
• R
  • ggplot2, tidyverse, grid
  • bio3d (for network analysis)

(See scripts/setup_hpc_env.sh for environment setup details)

Usage

Most analysis steps are driven by shell scripts in scripts/sh/. For example, to run the order parameter analysis:

bash scripts/sh/run_all_order_params.sh

Individual plotting scripts can be run directly if the data (XTC/GRO or extracted DAT files) is available in the expected systems/ directory structure.