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Shulin packages axonemal outer dynein arms for ciliary targeting. Mali GR, Ali FA et al. Science. 2021 Feb 26;371(6532):910-916.

Mechanism of membrane-tethered mitochondrial protein synthesis. Itoh Y, Andréll J et al. Science. 2021 Feb 19;371(6531):846-849.

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. Koenig PA, Das H et al. Science. 2021 Feb 12;371(6530):eabe6230.

Mitochondrial sorting and assembly machinery operates by β-barrel switching. Takeda H, Tsutsumi A et al. Nature. 2021 Feb 4;590(7844):163-169.

Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Hennell James R, Deme JC et al. Nat Microbiol. 2021 Feb;6(2):221-233.

See also: RCSB PDB Images
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News

December 11, 2020

The RBVI wishes you a safe and happy holiday season! See our 2020 card and the gallery of previous cards back to 1985.

November 4, 2020

New paper online: UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, et al. Protein Sci. 2020, in press.

September 23, 2020

Mac users: ChimeraX v1.1 does not work on MacOS 11.0 (Big Sur), but this problem has been fixed in v1.1.1 and the daily build.

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UCSF ChimeraX

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use. Commercial users, please see ChimeraX commercial licensing.

ChimeraX is developed with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases.

Feature Highlight

membrane protein with lipophilicity coloring

Coloring by Molecular Lipophilicity Potential

Molecular lipophilicity potential (MLP) can be calculated for a protein and displayed with surface coloring using the command mlp or the Molecule Display icon . The image shows the photosynthetic reaction center from a purple sulfur bacterium, with MLP coloring on the molecular surface and membrane boundaries from OPM (Orientations of Proteins in Membranes entry 1eys). Blue and red balls represent the cytoplasmic and periplasmic sides of the bacterial inner membrane, respectively. Parts of the L, M, and H chains span the membrane, whereas the cytochrome subunit sits on the periplasmic side, at the top. The surface coloring ranges from dark goldenrod for the most hydrophobic potentials, through white, to dark cyan for the most hydrophilic. Ligands including lipid, detergent, heme, and various other cofactors are shown as purple surfaces.

For image setup after the structure from OPM has been opened, see the command file mlp.cxc.

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Example Image

cyclodextrin pore

Cyclodextrin Pore

The outer-membrane protein CymA admits bulky molecules into the periplasmic space of Klebsiella oxytoca. Here, CymA (PDB 4d5d chain A) is depicted in a style reminiscent of a diagnostic X-ray, with transparent molecular surface and β-strand “ribs” in white. The protein has ingested α-cyclodextrin (top) and β-cyclodextrin (bottom), bound at the entry site and near the exit, respectively. Cyclodextrin carbon atoms are shown in blue-gray and oxygen atoms in brick red. For image setup, see the command file xray.cxc.

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