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   Articles with "density maps" as a keyword



Molstack—Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps

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recommendations! 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

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recommendations! 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

MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search

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recommendations! Published in 2024 at "Journal of Chemical Information and Modeling"

DOI: 10.1021/acs.jcim.3c02007

Abstract: Molecular Dynamics Flexible Fitting (MDFF) is a widely used tool to refine high-resolution structures into cryo-EM density maps. Despite many successful applications, MDFF is still limited by its high computational cost, overfitting, accuracy, and performance… read more here.

Keywords: density maps; molecular dynamics; flexible fitting; cryo density ... See more keywords

Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement

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recommendations! 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

Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features

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recommendations! Published in 2024 at "Nature Communications"

DOI: 10.1038/s41467-024-45861-4

Abstract: Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational… read more here.

Keywords: alignment; density maps; cryo; density ... See more keywords

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

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recommendations! Published in 2024 at "Nature Communications"

DOI: 10.1038/s41467-024-49647-6

Abstract: Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates… read more here.

Keywords: protein structure; density maps; structure modeling; density ... See more keywords

DeepSymmetry : Using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures

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recommendations! 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

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recommendations! 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

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recommendations! 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

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recommendations! 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

Monoenergetic reconstructions and iodine density maps for visualization of coronary artery stents using 8-cm dual-layer detector spectral computed tomography: an in vitro phantom study

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recommendations! Published in 2024 at "Quantitative Imaging in Medicine and Surgery"

DOI: 10.21037/qims-24-786

Abstract: Background The effectiveness of coronary computed tomography (CT) angiography in assessing stent restenosis is hindered by heavy metal artifacts. This study aimed to evaluate the image quality of monoenergetic reconstructions and iodine density map for… read more here.

Keywords: layer detector; density maps; group; dual layer ... See more keywords