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Biological molecules such as proteins and nucleic acids are responsible for all life activities in the cells, and dysfunction of these molecules can cause severe diseases. These are complex systems consisting of as many as millions of atoms and performing biological functions through dynamical interactions between molecules. Information on the structures of these biological molecules and their dynamics is essential to understand the mechanism of their functions, which can have a huge impact in medicinal applications, particularly in design of new drugs.The structures and dynamics of large biological complexes can be determined using a variety of experimental techniques, each provides information at different resolution. X-ray crystallography has been providing a large amount of structural information at detailed atomic levels. With recent progress in experimental techniques, Cryo Electron Microscopy (cryo-EM) may be used to obtain 3D structural models near atomic-resolution. In addition, raw data from cryo-EM may now comprise millions of two-dimensional (2D) images of single molecules, which may represent distinct conformations of the molecule. Therefore, dynamics information could also be extracted from the 2D data.X-ray free electron laser (XFEL) is another exciting new technology that could significantly extend our structural knowledge of biological systems. The first XFEL began operation in 2009 at the SLAC National Accelerator followed by SACLA at RIKEN in 2011. Strong laser light from XFEL enables the measurement of single molecular complexes, without necessity of crystallization. However, for biological systems, due to their low diffraction power, signal to noise ratio is extremely low and interpretation of the data remains challenging. Given progresses in experimental techniques such as Cryo-EM and XFEL, new computational methods are also now needed to process and interpret data (millions of 2D images) obtained from these single particle experiments. We will discuss the development of hybrid computational methods that combine molecular mechanics and image data processing algorithms to derive structural and dynamical information from cryo-EM and XFEL data.