This repository contains code to apply the ESPER method to quasi-continuum models of biomolecules exhibiting multiple degrees of freedom, as described in Seitz et al. (2022, IEEE TCI). As inputs into ESPER, detailed instructions are also provided for generating custom synthetic datasets with increasing complexity to mirror known cryo-EM image attributes.
Cryo-EM dataset of 80S ribosomes from yeast. This dataset has been described in Dashti et al. (2014, PNAS) "Trajectories of the ribosome as a Brownian nanomachine". In that study, a subset of the dataset was used to demonstrate the performance of a machine learning technique (now termed ManifoldEM) using manifold embedding to determine the energy landscape of a molecule. The dataset is re-analyzed in Seitz et al.