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The detection of secondary structure of proteins using three dimensional (3D) cryo-electron microscopy (cryo-EM) images is still a challenging task when the spatial resolution of cryo-EM images is at medium level (5–10Å). Prior researches focused on the usage of local features that may not capture the global information of image objects. In this study, we propose to use deep learning methods to extract...
Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive...
Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images...
The criteria used to determine the residue contact is a fundamental factor in deriving knowledge-based mean force potential energy for protein structures. A commonly used criterion for two residues in contact is to require the sidechain center distance or the Calpha atom distance to be within a predetermined cutoff distance. However, the anisotropic nature of the sidechains can result in error in...
We have developed an algorithm to assemble a loop in between two helices using the idea of the cyclic coordinate descent (CCD) that is an inverse kinematics approach in the field of robotics. Our method is a variant of the original CCD. It uses both the forward walk and the backward walk with different targets. A test of 20 cases suggests that the minimum root mean square deviation to native for the...
We have developed a new method for adding constraints derived from low resolution density maps to Rosetta ab initio prediction method. This method incorporates the geometrical constraints of the helix skeleton that can be detected from a low resolution density map. We propose a 2-stage approach to predict the backbone of a protein from a low resolution map. In stage one, a small set of possible topologies...
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