Structure of the human TRPM4 ion channel in a lipid nanodisc. Autzen HE, Myasnikov AG et al. Science. 2018 Jan 12;359(6372). pii: eaar4510.
Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus. Nakanishi A, Kishikawa JI et al. Nat Commun. 2018 Jan 8;9(1):89.
Development of a genetically encodable FRET system using fluorescent RNA aptamers. Jepsen MDE, Sparvath SM et al. Nat Commun. 2018 Jan 2;9(1):18.
Integrative structure modeling with the Integrative Modeling Platform. Webb B, Viswanath S et al. Protein Sci. 2018 Jan;27(1):245-258.
Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. D'Imprima E, Salzer R et al. eLife. 2017 Dec 27;6. pii: e30483.(Previously featured citations...)
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October 24, 2017
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For a nice 3D-printing protocol that uses Chimera, see 3D Printing of Biomolecular Models for Research and Pedagogy by Da Veiga Beltrame, Tyrwhitt-Drake, et al. today in JoVE!(Previous news...)
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.
Structures and their pocket measurements can be fetched directly from the Computed Atlas of Surface Topography of proteins (CASTp) database or read from local files previously returned by the CASTp server. In Chimera, the pockets are shown in a pocket list. Choosing rows in the list performs actions such as zooming in on pockets and selecting the surrounding atoms.
The figure shows the four largest pockets by volume identified by CASTp for PDB entry 1ovh (a cavity mutant of T4 lysozyme), shown in yellow, orange, pink, and magenta in order of decreasing volume. The largest is lysozyme's active site, with two openings. The second largest is the engineered cavity. Mutated positions are shown in red. Green balls are Cl– ions.(More features...)
Peroxiredoxins are enzymes that help cells cope with stressors such as high levels of reactive oxygen species. The image shows a decameric peroxiredoxin from human red blood cells (Protein Data Bank entry 1qmv), styled as a holiday wreath.
See also the RBVI holiday card gallery.