ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Croll TI. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6).
Modular assembly of the nucleolar pre-60S ribosomal subunit. Sanghai ZA, Miller L et al. Nature. 2018 Apr 5;556(7699):126-129.
Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule. Tsai JC, Miller-Vedam LE et al. Science. 2018 Mar 30;359(6383).
General prediction of peptide-MHC binding modes using incremental docking: A proof of concept. Antunes DA, Devaurs D et al. Sci Rep. 2018 Mar 12;8(1):4327.
Structure and conformational dynamics of the human spliceosomal Bact complex. Haselbach D, Komarov I et al. Cell. 2018 Jan 25;172(3):454-464.e11.See also: RCSB PDB Images
April 6, 2018
January 1, 2018
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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 licensing.
ChimeraX development is supported in part by the National Institutes of Health (NIGMS P41-GM103311).
Molecular lipophilicity potential (MLP) can be calculated for a protein and displayed with surface coloring using the command mlp. 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, see the command file mlp.cxc.More features...
KCNQ1 is the pore-forming subunit of a cardiac potassium channel. It binds to calmodulin, and mutations in either of these proteins can cause congenital long QT syndrome, a dangerous propensity for irregular heartbeats. In the image, a structure of the KCNQ1/calmodulin complex (PDB 5vms) has been assembled into the native tetrameric form with the sym command. The view is from the cytoplasmic side, with KCNQ1 shown as surfaces, calmodulin as cartoons, and calcium ions as balls. A pastel palette from ColorBrewer has been used to color the surfaces, darkened with color modify for the cartoons, and “rotated” 45° in hue for the ions. See the command file colormod.cxc.