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Recent Citations
A generalized knowledge-based discriminatory function for biomolecular interactions. Bernard B, Samudrala R Proteins. 2009 Jul;76(1):115-128.
Insights into positive and negative requirements for protein-protein interactions by crystallographic analysis of the Beta-Lactamase Inhibitory Proteins BLIP, BLIP-I and BLP. Gretes M, Lim DC et.al. J Mol Biol. 2009 Jun 5;389(2):289-305.
DOCK 6: Combining techniques to model RNA-small molecule complexes. Lang PT, Brozell SR et.al. RNA. 2009 Jun;15(6):1219-30.
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Ryan M, Diekhans M et.al. Bioinformatics. 2009 Jun 1;25(11):1431-2.
Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Xiang Y, Leiman PG et.al. Mol Cell. 2009 May 15;34(3):375-86.
(Previously featured citations...)Chimera Search
Google™ SearchNews
April 24, 2009
The LabelHash server searches the PDB for matches to a user-specified 3D motif (pattern of residues). Results are shown with Chimera images and can be downloaded for local viewing with the Chimera extension ViewMatch. LabelHash and ViewMatch are provided by the Kavraki Lab at Rice University.
April 17, 2009
The LS-SNP/PDB database features Chimera images of human nonsynonymous SNP locations in protein structures and molecular surfaces colored by sequence conservation and electrostatic potential. This database is provided by the Karchin Lab at Johns Hopkins University.
December 9, 2008
Chimera production release 1.3 is available for all platforms, including Mac Aqua (does not require X windows). It addresses Microsoft Windows graphics drivers problems and will be the last production release for IRIX and Tru64. See the release notes for changes since the previous production release (July 2008).
(Previous news...)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, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the NIH National Center for Research Resources (grant P41-RR01081).
Feature Highlight
The program DOCK calculates possible binding orientations, given the structures of "ligand" and "receptor" molecules. Typically, a large database of small molecule structures is searched for compounds that may bind the receptor. The Chimera extension ViewDock facilitates interactive selection of promising compounds from the output of DOCK. The molecules can be viewed in the context of the binding site and optionally, screened by number of hydrogen bonds to the receptor. The Dock Prep extension prepares a receptor for input to a docking program by adding hydrogens, assigning partial charges, and performing other related tasks.
(More features...)Gallery Sample
This image of a clathrin cage uses flat shading and edge highlighting. It is a copy of a PDB molecule of the month image made by Graham Johnson and Dave Goodsell. David Goodsell pioneered this visualization style. This image was made with the Multiscale tool and silhouette edging (enabled with menu entry Tools / Viewing Controls / Effects). There is no Chimera control for achieving the flat shading. That was done by opening a Python script lightsout.py.
Protein Data Bank model 1xi4.
(More samples...)