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

Abstract

Molecular dynamics (MD) simulations are a central tool for investigating biomolecularflexibility, conformational transitions, recognition, and membrane-associated behavior, yettrajectory post-processing often remains fragmented across command-line programs, customscripts, and disconnected plotting environments. Here we present ShineMD, a local pure-R/Shiny application for integrated analysis of AMBER trajectory projects within a singlegraphical 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, structuralclustering, and representative-structure export in a coherent script-free workflow. Theinterface also incorporates contextual information buttons and guided elements that helpmake routine MD post-processing more approachable for users with different levels ofcomputational experience. Core conformational descriptors benchmarked against CPPTRAJshowed excellent agreement across all tested observables (Pearson r > 0.994 for RMSD,RMSF, and radius of gyration). Extended MDAnalysis-based validation further supportedrepresentative PCA, interaction/contact, clustering, and membrane-analysis outputs. Theapplication is illustrated with two representative systems: a 100 ns soluble BChE-peptideinhibitor complex (77 671 atoms, five trajectory segments) and a 500 ns membraneinteractinglipopeptide in a POPE/POPG bilayer (26 677 atoms), covering distinct butcommon MD use cases. ShineMD is distributed as a single-file R/Shiny application underthe MIT license and is available at https://github.com/sanchisivan/ShineMD.