Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy
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 …
microscopy (cryo-EM) images is still a challenging task when the spatial resolution of cryo …
Tracing beta strands using StrandTwister from cryo-EM density maps at medium resolutions
Major secondary structure elements such as α helices and β sheets can be computationally
detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5 …
detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5 …
Mathematical and Machine Learning Approaches for Classification of Protein Secondary Structure Elements from Cα Coordinates
Determining Secondary Structure Elements (SSEs) for any protein is crucial as an
intermediate step for experimental tertiary structure determination. SSEs are identified using …
intermediate step for experimental tertiary structure determination. SSEs are identified using …
A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation
Background Cryo-electron tomography is an important and powerful technique to explore
the structure, abundance, and location of ultrastructure in a near-native state. It contains …
the structure, abundance, and location of ultrastructure in a near-native state. It contains …
Structural modeling from electron microscopy data
Cryo‐electron microscopy is a powerful technique for the determination of three‐
dimensional (3D) structures of macromolecular machines, as it provides functional …
dimensional (3D) structures of macromolecular machines, as it provides functional …
Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm
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 …
scale images of protein molecules. In contrast to other experimental techniques, cryo …
Exploratory studies detecting secondary structures in medium resolution 3D Cryo-EM images using deep convolutional neural networks
Cryo-electron microscopy (cryo-EM) is an emerging biophysical technique for structural
determination of protein complexes. However, accurate detection of secondary structures is …
determination of protein complexes. However, accurate detection of secondary structures is …
Constrained cyclic coordinate descent for cryo-EM images at medium resolutions: beyond the protein loop closure problem
The cyclic coordinate descent (CCD) method is a popular loop closure method in protein
structure modeling. It is a robotics algorithm originally developed for inverse kinematic …
structure modeling. It is a robotics algorithm originally developed for inverse kinematic …
Comparing an atomic model or structure to a corresponding cryo-electron microscopy image at the central axis of a helix
Three-dimensional density maps of biological specimens from cryo-electron microscopy
(cryo-EM) can be interpreted in the form of atomic models that are modeled into the density …
(cryo-EM) can be interpreted in the form of atomic models that are modeled into the density …
Analytical approaches to improve accuracy in solving the protein topology problem
To take advantage of recent advances in genomics and proteomics it is critical that the three-
dimensional physical structure of biological macromolecules be determined. Cryo-Electron …
dimensional physical structure of biological macromolecules be determined. Cryo-Electron …