ERMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems.

ABSTRACT: Understanding molecular flexibility and dynamics across different structural ensembles is essential for interpreting the behavior of complex biological systems. Here, we introduce eRMSF, a fast and user-friendly Python package built with MDAKit from MDAnalysis, designed to perform ensemble-based root mean square fluctuation (RMSF) analyses. Unlike traditional approaches limited to molecular dynamics trajectories, eRMSF extends flexibility analysis to ensembles generated by different methods, such as MD simulations, BioEmu (a deep learning tool for equilibrium ensemble prediction), subsampled AlphaFold2 (AlphaFold ensemble generation), and other computational or experimental sources. By enabling RMSF calculations across heterogeneous ensembles, eRMSF provides a unified framework to evaluate

SUBMITTER: Arantes PR 

PROVIDER: S-EPMC12690589 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature