ConformaLens: conformational states in Adaptive Molecular Dynamics

Authors

Hossein Fathollahian (University of Illinois Chicago), Siyuan Zhao (University of Illinois Chicago), Marziye Salahshour (Rush University), Saeed Boorboor (University of Illinois Chicago), G. Elisabeta Marai (University of Illinois at Chicago)

Abstract

Adaptive molecular dynamics (MD) ensembles capture complex conformational behavior, but interpreting Markov State Model (MSM) assignments across many trajectories, frames, states, and ligand conditions remains challenging. We present ConformaLens, a linked visual analytics application for comparing free, TMP-bound, and SPA-bound Aβ42 simulations. Its coordinated timeline, transition footprints, interaction glyphs, and 3D structural views connect ensemble-level MSM dynamics with ligand effects and residue-level evidence, revealing representative states and residue-residue or residue-ligand differences across trajectories and frames.