Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions

Cryo-electron Microscopy (cryoEM) is an advanced imaging technique that produces volume maps at different resolutions. This technique is capable of visualizing large molecular complexes such as viruses and ribosomes. At the medium resolutions, such as 5 to 10Å, the location and orientation of the secondary structure elements (SSEs) can be computationally identified. However, there is no registration between the detected SSEs and the protein sequence, and therefore it is challenging to derive the atomic structure from such volume data. We present, in this paper, the preliminary results of the full-atom protein chains using our de novo modeling framework. The framework has multiple components including the ranking of topologies, the construction of helices and loops along the density traces, and the energy evaluation of the structure. A test containing thirteen simulated density maps and two experimentally derived density maps show that the true topology was ranked among the top 35 of the huge topological space. The best atomic model of the true topology was ranked within the top 40 for twelve of the fifteen proteins tested. The average backbone RMSD100 of these models is about 4Å for the fifteen proteins.