LAUSR

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

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0 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

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

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0 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

Thresholding of cryo-EM density maps by false discovery rate control

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1 Published in 2019 at "IUCrJ"

DOI: 10.1107/s2052252518014434

Abstract: The interpretation of cryo-EM density by atomic models remains a daunting task owing to the identification of appropriate threshold levels at low signal-to-noise ratios in high-resolution shells and weak structural features. It is shown that… read more here.

Keywords: discovery rate; false discovery; cryo density;

Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

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0 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

Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution

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1 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