ShineMD: an automated pure-R platform with a graphical user interface for integrated analysis of AMBER molecular...

Molecular dynamics (MD) simulations are a central tool for investigating biomolecular flexibility, conformational transitions, recognition, and membrane-associated behavior, yet trajectory post-processing often remains fragmented across command-line programs, custom scripts, and disconnected plotting environments. Here we present ShineMD, a local pure-R/Shiny application for integrated analysis of AMBER trajectory projects within a single graphical interface. The platform handles segmented production trajectories natively, preserves full segment-level frame provenance, and combines conformational descriptors, dimensionality reduction, interaction analysis, membrane-oriented metrics, structural clustering, and representative-structure export in a coherent script-free workflow. The interface also incorporates contextual information buttons and guided elements that help make routine MD post-processing more approachable for users with different levels of computational experience. Core conformational descriptors benchmarked against CPPTRAJ showed excellent agreement across all tested observables (Pearson r > 0.994 for RMSD, RMSF, and radius of gyration). Extended MDAnalysis-based validation further supported representative PCA, interaction/contact, clustering, and membrane-analysis outputs. The application is illustrated with two representative systems: a 100 ns soluble BChE-peptide inhibitor complex (77 671 atoms, five trajectory segments) and a 500 ns membrane-interacting lipopeptide in a POPE/POPG bilayer (26 677 atoms), covering distinct but common MD use cases. ShineMD is distributed as a single-file R/Shiny application under the MIT license and is available at https://github.com/sanchisivan/ShineMD.