EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
… chain D corresponding to the maps in b. Colors correspond to the frames shown in b. (d)
Proteasome chain 1 residue Gln36 shown in density (isolevel 0.32) as in b. (e) EMRinger plots …
Proteasome chain 1 residue Gln36 shown in density (isolevel 0.32) as in b. (e) EMRinger plots …
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
… The results indicate that our refinement method is not particularly sensitive to the extent of
B-factor sharpening, behaving similarly over a range of sharpening values Figure 2 continued …
B-factor sharpening, behaving similarly over a range of sharpening values Figure 2 continued …
[HTML][HTML] Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1)
assess the quality of models that can be produced from cryogenic electron microscopy (…
assess the quality of models that can be produced from cryogenic electron microscopy (…
Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline
BA Barad, M Medina, D Fuentes, RL Wiseman… - Journal of Cell …, 2023 - rupress.org
… BA Barad is supported by an American Cancer Society postdoctoral fellowship (PF-21-075-01-CCB).
RL Wiseman is supported by the National Institutes of Health grant R01NS095892. …
RL Wiseman is supported by the National Institutes of Health grant R01NS095892. …
Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting
… (B) The library contains most codon substitutions and almost all are associated with
multiple barcodes. A slight GC bias is seen in the cloning. WT codons are shown in green and …
multiple barcodes. A slight GC bias is seen in the cloning. WT codons are shown in green and …
XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction
…, K Koiwai, AS Brewster, BA Barad… - Proceedings of the …, 2017 - National Acad Sciences
… explain the crystallographic positions of the half-occupancy waters within the symmetry
constraints of the I4 space group; the waters within network A are too close to those in network B …
constraints of the I4 space group; the waters within network A are too close to those in network B …
Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme
… b, The area under the averaged difference scattering curve in the q = 0.03–0.05 Å −1 region
was integrated for all measured pump–probe time delays, and the resulting absolute values …
was integrated for all measured pump–probe time delays, and the resulting absolute values …
[HTML][HTML] Overcoming resolution attenuation during tilted cryo-EM data collection
…, M Mietzsch, JA Hull, S Hoshika, BA Barad… - Nature …, 2024 - nature.com
… . b–h Individual steps were added to the workflow, and improvements in resolution are plotted
as … . b–h Individual steps were added to the workflow and improvements in resolution are …
as … . b–h Individual steps were added to the workflow and improvements in resolution are …
Nanoscale details of mitochondrial constriction revealed by cryoelectron tomography
Mitochondria adapt to changing cellular environments, stress stimuli, and metabolic
demands through dramatic morphological remodeling of their shape, and thus function. Such …
demands through dramatic morphological remodeling of their shape, and thus function. Such …
[HTML][HTML] CellPAINT: turnkey illustration of molecular cell biology
CellPAINT is an interactive digital tool that allows non-expert users to create illustrations of
the molecular structure of cells and viruses. We present a new release with several key …
the molecular structure of cells and viruses. We present a new release with several key …