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Targeting protein-ligand neosurfaces with a generalizable deep learning tool. Marchand A, Buckley S et al. Nature. 2025 Mar 13;639(8054):522–531.
Structural insights into RNA cleavage by PIWI Argonaute. Li Z, Xu Q et al. Nature. 2025 Mar 6;639(8053):250–259.
Plant pathogenic fungi hijack phosphate signaling with conserved enzymatic effectors. McCombe CL, Wegner A et al. Science. 2025 Feb 28;387(6737):955-962.
Antiviral signaling of a type III CRISPR-associated deaminase. Li Y, Li Z et al. Science. 2025 Feb 21;387(6736):eadr0393.
The structure of apolipoprotein B100 from human low-density lipoprotein. Berndsen ZT, Cassidy CK. Nature. 2025 Feb 20;638(8051):836–843.
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March 1, 2025
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December 25, 2024
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December 12, 2024
The ChimeraX 1.9 production release is available! See the change log for what's new.
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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 ChimeraX commercial licensing.
ChimeraX is developed with support from National Institutes of Health R01-GM129325.
ChimeraX on Bluesky:
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Feature Highlight
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Rotamers is an interface for showing amino acid sidechain rotamers and optionally replacing the original sidechain, also implemented as the swapaa command. The rotamers can be shown all at once, as in the figure, or individually by choosing rows in the dialog.
The figure shows binding-site residues of the thyroid hormone receptor β with hormone bound, PDB 3gws. Rotamers for the hormone-resistance mutations N331H and L346R are shown as partially transparent sticks, with H-bonds (light blue dashed line) and clashes (light purple dashed lines) calculated for the histidine rotamers at position 331. The rotamer-list dialog for this position is also shown. Command script rotamers.cxc contains the initial, noninteractive part of the setup.
These mutations are described in Cardoso et al., Endocrine (2020). Although one histidine rotamer may be able to form the same pocket-stabilizing H-bond as the wild-type asparagine, it also clashes with several atoms (third row in the dialog). H-bonds and clashes are not shown for the arginine rotamers at 346, but they all clash significantly with the hormone and/or other pocket atoms.
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Example Image
Atomic B-factor values are read from PDB and mmCIF input files and assigned as attributes that can be shown with coloring and used in atom specification. This example shows B-factor variation within a structure of the HIV-1 protease bound to an inhibitor (PDB 4hvp). For complete image setup, including positioning, color key, and label, see the command file bfactor.cxc.
Additional color key examples can be found in tutorials: Coloring by Electrostatic Potential, Coloring by Sequence Conservation
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