Minisymposium Presentation

To fully understand biological functions, high-resolution biomolecular structures are required, which can be obtained through diverse experimental methods such as X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM) and computationally via AlphaFold2. While these techniques provide valuable structural insights, elucidating the dynamic of these biomolecules is also essential, given that some molecules display inherent structural flexibility. A thorough comprehension of such dynamics involves characterizing various conformational states at the atomic level. Raw experimental data from cryo-EM consist of millions of 2D images that represent specific views of a biomolecule, potentially capturing different conformational states, as each image may correspond to a distinct conformation. To connect these 2D images with atomic models, Molecular Dynamics (MD) simulations can be employed to generate conformations that align with the observed data. Due to the large scale of cryo-EM datasets, processing them often demands high-performance computing. In this talk, I will present our work and the implementation of MDSPACE, a biased MD simulation method, for conducting such analyses on the Fukagu system.