User profiles for B. Barad

Benjamin A. Barad

- Verified email at ohsu.edu - Cited by 1543

bharat bidhan barad

- Verified email at iitbhilai.ac.in - Cited by 26

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

BA Barad, N Echols, RYR Wang, Y Cheng, F DiMaio… - Nature …, 2015 - nature.com
… 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 …

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

RYR Wang, Y Song, BA Barad, Y Cheng, JS Fraser… - Elife, 2016 - elifesciences.org
… 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 …

[HTML][HTML] Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

…, PD Adams, PV Afonine, ML Baker, BA Barad… - Nature …, 2021 - nature.com
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 (…

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. …

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

D Mavor, K Barlow, S Thompson, BA Barad, AR Bonny… - Elife, 2016 - elifesciences.org
… (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 …

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

Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme

MC Thompson, BA Barad, AM Wolff, H Sun Cho… - Nature …, 2019 - nature.com
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 …

[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 …

Nanoscale details of mitochondrial constriction revealed by cryoelectron tomography

SK Mageswaran, DA Grotjahn, X Zeng, BA Barad… - Biophysical …, 2023 - cell.com
Mitochondria adapt to changing cellular environments, stress stimuli, and metabolic
demands through dramatic morphological remodeling of their shape, and thus function. Such …

[HTML][HTML] CellPAINT: turnkey illustration of molecular cell biology

…, L Autin, D Fuentes, M Maritan, BA Barad… - Frontiers in …, 2021 - frontiersin.org
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 …