ShineMD is an interactive R Shiny application for molecular dynamics (MD) trajectory analysis and visualization. It provides a fully graphical, browser-based interface for processing and exploring MD simulations — no scripting required.
The app is designed to bring routine trajectory post-processing into a single local workflow. Instead of moving between command-line tools, custom scripts, spreadsheets, and plotting software, users can load a project folder and compute structural descriptors, dimensionality reduction, membrane-oriented analyses, interaction profiles, clustering, and representative-structure exports from one interface.
ShineMD is especially useful for users who want publication-ready figures and interpretable analysis panels without building custom pipelines for every new system. It supports both general soluble biomolecular systems and more specialized cases such as membrane-active peptides, lipid bilayers, and protein-peptide interaction studies.
Developed at the Laboratory of Bioactive Peptides (LPB), Faculty of Biochemistry and Biological Sciences, National University of the Littoral (UNL), Santa Fe, Argentina.
Project tab overview showing folder detection, run settings, and the main workflow entry point.
| Category | Analyses |
|---|---|
| Structural | RMSD, RMSF, Radius of Gyration |
| Dimensionality reduction | PCA, Free Energy Landscape (FEL) |
| Membrane biophysics | Bilayer thickness, Area per lipid, Density profiles, Lipid C-C segment order |<S_CC>|, Lipid enrichment, COM distances |
| Interactions | Contact time series, Residue occupancy, Contact map (heatmap), H-bond proxy analysis |
| Clustering | Hierarchical (Ward.D2) and k-medoids (PAM), Structure export (medoids, centroids, single frames) |
| Reproducibility | Session info export, package version tracking |
All plots are interactive (pan, zoom, hover), support dark/light themes, and can be exported as PDF, PNG, or SVG. Data tables are downloadable as CSV, and the app also helps preserve reproducibility through export helpers and session information tracking.
ShineMD works with AMBER simulation files:
| File | Extension |
|---|---|
| Topology | .prmtop, .parm7 |
| Trajectory | .nc (NetCDF) |
| Optional reference structure | .pdb, .rst7, .inpcrd, .crd |
Multiple trajectory segments (e.g. prod_1.nc, prod_2.nc, …) are automatically detected, naturally sorted, and can be concatenated into a continuous timeline.
The repository includes compact AMBER example datasets:
trpzip2.ff10.mbondi.parm7trpzip2.gb.nctrpzip2.1LE1.1.rst7
These files come from the official AMBER CPPTRAJ Tutorial C1 ("RMSD Analysis in CPPTRAJ") and are useful for quick app demos and for validating ShineMD results against the tutorial workflow and the CPPTRAJ reference implementation.
Source: https://ambermd.org/tutorials/analysis/tutorial1/
The repository also includes a reduced membrane example in examples/membrane_pep/:
mem_pep.prmtopmem_pep.nc
This dataset is derived from the membrane system used as an example in the published ShineMD paper, but the lipopeptide was truncated to its last 4 residues because the full system is still unpublished. The included trajectory is frame-reduced by retaining one of every 100 original frames to limit repository size. It is intended for testing membrane-specific features such as density profiles and lipid C-C segment order, not for exact reproduction of the full production trajectory. Recommended settings are documented in examples/membrane_pep/README.md.
The repository also includes a reduced BChE-peptide example in examples/bche_pep/:
bche_pep.prmtopbche_pep.nc
This dataset is derived from the BChE-peptide system used as an example in the published ShineMD paper. The included trajectory is frame-reduced by retaining one of every 100 original frames to limit repository size, and is intended for testing structural A/B metrics, complex-level clustering, and the Interactions tab. Recommended reproduction settings are documented in examples/bche_pep/README.md.
ShineMD runs in R (≥ 4.0 recommended). Install all required packages from CRAN:
install.packages(c(
"shiny", "shinydashboard", "shinyjs", "shinyWidgets", "shinyFiles",
"plotly", "ggplot2", "DT", "htmlwidgets",
"bio3d", "ncdf4", "fs"
))Clone the repository:
git clone https://github.com/sanchisivan/ShineMD.gitOpen the ShineMD/ folder in RStudio or start R in that folder, then run:
shiny::runApp()In RStudio, you can also open app.R and click Run App. The app will open in your default web browser. If not, navigate to the URL shown in the R console (e.g. http://127.0.0.1:XXXX).
A full User Manual is available in this repository:
The manual covers every tab, parameter, analysis, and export option in detail, along with tips and troubleshooting guidance.
ShineMD/
├── app.R # Main application (UI + server)
├── README.md
├── USER_MANUAL.md # Complete user documentation
├── examples/ # Example datasets and provenance notes
├── CITATION.cff
├── LICENSE
├── .gitignore
└── www/ # Static assets (logos)
If you use ShineMD in academic work, please cite the peer-reviewed article:
Sanchis I, Siano AS. ShineMD: an automated pure-R platform with a graphical user interface for integrated analysis of AMBER molecular dynamics trajectories. Computational Biology and Chemistry. 2026; Article 109254. https://doi.org/10.1016/j.compbiolchem.2026.109254
The CITATION.cff file includes the publication metadata and DOI for reference managers and GitHub's Cite this repository feature.
Laboratory of Bioactive Peptides (LPB)
Faculty of Biochemistry and Biological Sciences (FBCB)
National University of the Littoral (UNL) · Santa Fe, Argentina
| Dr. Iván Sanchis (app development) | sanchisivan@fbcb.unl.edu.ar |
| Prof. Álvaro Sebastián Siano (group leader) | asiano@fbcb.unl.edu.ar |
MIT License — see LICENSE for details.