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The Dundee Resource for Sequence Analysis and Structure Prediction. MacGowan SA, Madeira F et al. Protein Sci. 2020 Jan;29(1):277-297.

Cryo-EM structures of apo and antagonist-bound human Cav3.1. Zhao Y, Huang G et al. Nature. 2019 Dec 19;576(7787):492-497.

Experimental evidence of solvent-separated ion pairs as metastable states in electrostatic interactions of biological macromolecules. Yu B, Pettitt BM, Iwahara J. J Phys Chem Lett. 2019 Dec 19;10(24):7937-7941.

Structure and drug resistance of the Plasmodium falciparum transporter PfCRT. Kim J, Tan YZ et al. Nature. 2019 Dec 12;576(7786):315-320.

A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Steichen JM, Lin YC et al. Science. 2019 Dec 6;366(6470):eaax4380.

(Previously featured citations...)

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News

November 13, 2019

Chimera production release 1.14 is now available. See the release notes for what's new.

September 21, 2019

A production release candidate (version 1.14) is available; please try it and report any problems. See the release notes for what's new.

November 17, 2018

Chimera production release 1.13.1 is now available; see the release notes for what's new. The Mac version requires OS 10.10 or later.

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Upcoming Events

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), supported in part by the National Institutes of Health (P41-GM103311).

UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.

Feature Highlight

mda p08648 limit 4 percent 50

Find and Summarize Structures for a Sequence

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.

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Gallery Sample

Peroxiredoxin Wreath

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.

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