Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism. Whicher JR, MacKinnon R. Science. 2016 Aug 12;353(6300):664-9.
The acidic domain is a unique structural feature of the splicing factor SYNCRIP. Beuck C, Williamson JR et al. Protein Sci. 2016 Aug;25(8):1545-50.
HU multimerization shift controls nucleoid compaction. Hammel M, Amlanjyoti D et al. Sci Adv. 2016 Jul 29;2(7):e1600650.
Tetracarbalane structures: nido polyhedra and non-spherical deltahedra. Attia AA, Lupan A, King RB. Dalton Trans. 2016 Jul 28;45(28):11528-39.
Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria. Mühleip AW, Joos F et al. Proc Natl Acad Sci USA. 2016 Jul 26;113(30):8442-7.(Previously featured citations...)
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August 26, 2016
A production release candidate (version 1.11.1) is now available. Please try it and report any problems. See the release notes for what's been fixed since 1.11. The 1.11 release series will be the last to support 32-bit builds.
July 15, 2016
June 23, 2016
PLOS Computational Biology announces winning T-shirt design created by Luigi Di Costanzo (RCSB Protein Data Bank) using UCSF Chimera.(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, non-profit, 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. It is in early development and not yet publicly released, with release anticipated sometime in 2016.
One use of Multidomain Assembler is to set up comparative modeling and concatenation of existing structures to generate a full-length model of a multidomain protein. However, even without model-building, the byproduct is also useful: a visual summary of the structures available for a query sequence, optionally filtered by criteria such as BLAST score and % identity, laid out horizontally in approximate N→C order relative to the query. Overlapping hits are stacked vertically, and segments without structural coverage are indicated with spheres. By default, the multiple sequence alignment of the hits to the query is also displayed.
The figure shows the results of command:
mda p08648 ~/Desktop/MDA limit 4 percent 50
with sequence mismatches in red and molecules other than the hit chains in blue. Text and pointers have been added with 2D Labels.
Multidomain Assembler is described in a paper.(More features...)
Side-by-side views of a potassium channel structure (Protein Data Bank entry 1bl8) showing different approaches to cavity detection. On the left are molecular surface patches corresponding to the structure's two largest pockets by MS volume in the Computed Atlas of Surface Topography of proteins (CASTp) database. On the right is a tunnel in blue identified by the MolAxis server. Simple editing converted MolAxis output into a BILD file for display in Chimera. (More samples...)