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Tiwari, S. P.; Tama, F. & Miyashita, O. Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. BMC bioinformatics, 2018, 19, 320


Advancements in biophysical experimental techniques have pushed the limits in terms of the types of phenomena that can be characterized, the amount of data that can be produced and the resolution at which we can visualize them. Single particle techniques such as Electron Microscopy (EM) and X-ray free electron laser (XFEL) scattering require a large number of 2D images collected to resolve three-dimensional (3D) structures. In this study, we propose a quick strategy to retrieve potential 3D shapes, as low-resolution models, from a few 2D experimental images by searching a library of 2D projection images generated from existing 3D structures. We developed the protocol to assemble a non-redundant set of 3D shapes for generating the 2D image library, and to retrieve potential match 3D shapes for query images, using EM data as a test. In our strategy, we disregard differences in volume size, giving previously unknown structures and conformations a greater number of 3D biological shapes as possible matches. We tested the strategy using images from three EM models as query images for searches against a library of 22750 2D projection images generated from 250 random EM models. We found that our ability to identify 3D shapes that match the query images depends on how complex the outline of the 2D shapes are and whether they are represented in the search image library. Through our computational method, we are able to quickly retrieve a 3D shape from a few 2D projection images. Our approach has the potential for exploring other types of 2D single particle structural data such as from XFEL scattering experiments, for providing a tool to interpret low-resolution data that may be insufficient for 3D reconstruction, and for estimating the mixing of states or conformations that could exist in such experimental data.




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