Visualizing density maps with UCSF Chimera.

By Thomas D. Goddard, Conrad C. Huang, T. Ferrin. Journal of Structural Biology, 2007

902 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

View Paper: https://www.semanticscholar.org/paper/a9e6a81c5b3a39152fd4676033c38aa68cd7ae95

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Citations in the corpus

Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism (2020, methodology): “DOI: https://doi.org/10.7554/eLife.56185 12 of 23 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Software, algorithm MUSCLE DOI: 10.1093/ nar/gkh340 RRID:SCR_011812 https://www. drive5.com/ muscle/ Software, algorithm Fiji other RRID:S”
Complete subunit architecture of the proteasome regulatory particle (2012, positive): “UCSF Chimera was used for volume segmentation, atomic coordinate docking, and figure generation 47 .”
UCSF ChimeraX: Meeting modern challenges in visualization and analysis (2018, background): “ChimeraX builds on our highly successful UCSF Chimera visualization system, 19–22 which was first released in 2002 and has been cited by over 11,800 journal articles, downloaded over 620,000 times, and has over 22,200 registered users (even though registration is voluntary and does not affect…”
Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion (2020, positive): “Figures were generated using UCSF ChimeraX (Goddard et al., 2018).”
3D architecture of DNA Pol α reveals the functional core of multi-subunit replicative polymerases (2009, positive): “The final volumes and fitting were visualised using UCSF Chimera (Goddard et al, 2007).”
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “These capabilities augment over 100 tools already provided by Chimera for the interactive analysis of atomic models, density maps, and protein sequences (Couch et al., 2006; Goddard et al., 2005, 2007; Meng et al., 2006; Morris et al., 2007; Pettersen et al., 2004; Pintilie et al., 2010).”
Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy (2016, methodology): “UCSF Chimera 66 and Coot 22,67 were used to fit atomic models into the cryo-EM map.”
Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein (2020, methodology): “CryoEM model building and analysis UCSF Chimera (Goddard et al., 2007) and Coot were used to fit atomic models (PDB 6NB6) into the cryoEM map.”
Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance (2016, methodology): “For difference maps, the full V/A-ATPase atomic model was converted to a density map with the molmap function in UCSF Chimera.”
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions (2010, methodology): “We use the gradient-based method in Chimera because we found it to be robust and fast.”