Molstack—Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps
Sign Up to like & getrecommendations! Published in 2018 at "Protein Science"
DOI: 10.1002/pro.3272
Abstract: Our understanding of the world of biomolecular structures is based upon the interpretation of macromolecular models, of which ∼90% are an interpretation of electron density maps. This structural information guides scientific progress and exploration in… read more here.
Keywords: interpretation; molstack; density maps; evidence ... See more keywords
Determination of chemical identity and occupancy from experimental density maps
Sign Up to like & getrecommendations! Published in 2018 at "Protein Science"
DOI: 10.1002/pro.3325
Abstract: Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large… read more here.
Keywords: determination chemical; density maps; density; chemical identity ... See more keywords
Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.9b00932
Abstract: Cryo-EM has become one of the prime methods for protein structure elucidation, frequently yielding density maps with near-atomic or medium resolution. If protein structures cannot be deduced unambiguously from the density maps, computational structure refinement… read more here.
Keywords: protein; nmr chemical; density maps; density ... See more keywords
DeepSymmetry : Using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz454
Abstract: MOTIVATION Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these structures contain structural repetitions or internal symmetries. To understand… read more here.
Keywords: structural repetitions; convolutional networks; using convolutional; internal symmetries ... See more keywords
Residue Assignment in Crystallographic Protein Electron Density Maps With 3D Convolutional Networks
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Access"
DOI: 10.1109/access.2022.3156108
Abstract: This work proposes a neural network architecture, called 3D FC-DenseNet, for assigning amino acid labels to X-ray crystallographic electron density maps without relying on the amino acid sequence of proteins. The 3DFC-DenseNet is able to… read more here.
Keywords: protein electron; amino acid; density maps; electron density ... See more keywords
Single Shot Residue Localization and Classification in Crystallographic Electron Density Maps
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Access"
DOI: 10.1109/access.2022.3213670
Abstract: Despite constant advances in X-ray crystallography, the resolution of the acquired electron density maps still poses a serious limit on protein protein structural model building efforts. Furthermore, the currently available toolkits require hours or even… read more here.
Keywords: density maps; single shot; electron density; crystallographic electron ... See more keywords
Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps
Sign Up to like & getrecommendations! Published in 2017 at "BioMed Research International"
DOI: 10.1155/2017/1793213
Abstract: Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although α-helices can be detected from density maps at 5–8 Å resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands.… read more here.
Keywords: cryo density; density maps; density; traces beta ... See more keywords
Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps
Sign Up to like & getrecommendations! Published in 2022 at "Biomolecules"
DOI: 10.3390/biom12060773
Abstract: Single-particle electron cryomicroscopy (cryoEM) has become an indispensable tool for studying structure and function in macromolecular assemblies. As an integral part of the cryoEM structure determination process, computational tools have been developed to build atomic… read more here.
Keywords: density; beyond backbone; density maps; backbone next ... See more keywords
Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution
Sign Up to like & getrecommendations! Published in 2022 at "Biomolecules"
DOI: 10.3390/biom12091290
Abstract: Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3–5… read more here.
Keywords: density; building protein; cryo density; density maps ... See more keywords
Effects of a Low-Pass Filter on the Classification of Protein Electron-Density Maps in Terms of Structural Polymorphism using Manifold Learning: A Simulation Study for Cryo-Electron Microscopy Experiments
Sign Up to like & getrecommendations! Published in 2019 at "Journal of the Physical Society of Japan"
DOI: 10.7566/jpsj.88.094801
Abstract: Analyzing the structure of proteins in terms of their structural polymorphism has been recently performed using their two-dimensional electron-density maps obtained through cryo-electron microscopy... read more here.
Keywords: microscopy; density maps; electron; electron density ... See more keywords