See also: Web services used by UCSF Chimera, sites that provide Chimera Web data, and Chimera plug-ins on the Web
Experimentally determined protein structures, divided into domains as defined by SCOP (Structural Classification of Proteins).
Conformational Dynamics Data Bank
Provides conformational dynamics of proteins and protein assemblies from normal mode analysis. CDDB uses Chimera to compute and export surface mesh; data files include density maps that can be viewed in Chimera.
Cube-DB Database of pre-evaluated conservation and specialization scores for multi-member families of human proteins. Includes downloadable Chimera session files with color-coded structures. Cube-DB is described in Zhang et al., Nucleic Acids Res 40:D490 (2012).
for Aligned Ribosomal Complexes (DARC)
Ribosomal structures from the PDB and EMDB aligned into a common frame of reference. Data processed with Chimera, can be viewed with Chimera. DARC is described in Jarasch et al., Nucleic Acids Res 40:D495 (2012).
This site contains 3D density maps obtained by electron microscopy in CCP4 format that can be shown with Chimera Volume Viewer.
Presents images, movies, Chimera sessions and details about electron microscopy density maps from the EM DataBank.
Growth Factor Mutation Database
Searchable/browsable repository of IGF mutants and associated receptor-binding data; mutations mapped to structure in Chimera images.
A database of human nonsynonymous single-nucleotide polymorphisms (nsSNPs) mapped onto protein structures. Chimera-generated images show SNP locations in the structures and molecular surfaces colored by superfamily sequence conservation and DelPhi-computed electrostatic potential.
A database of three-dimensional protein models calculated by comparative modeling.
A database of mouse mutations and phenotypes induced by ENU. Many of the allele pages include molecular structure images and movies made in Chimera.
A database that associates human SNP and mutation data with protein structures. The authors provide a Chimera extension to access the data via web services.
Comprehensive information and tools for the study of protein post-translational modifications; includes scripts for visualization in Chimera.
Protein Data Bank (PDB)
Experimentally determined protein and nucleic acid structures. Display PDB format files.
Structure-Function Linkage Database
Connecting enzyme structure and function at the level of conserved partial chemical reactions.
UCSC Genome Browser
Chimera links are provided in UCSC Gene pages (see example) and SNP track details pages. Clicking a Chimera link displays the corresponding structure with nonsynonymous SNP residues colored and labeled with the dbSNP identifier.
Crystallographic electron density maps for protein data bank x-ray structures. Display O, CCP4, or CNS format density maps with Chimera Volume Viewer.
Atomic resolution virus capsid structures. Some of the capsid images on this site are made with the Chimera Multiscale Models tool.
Molecular force field and dynamics simulations. Display trajectories with the Chimera MD Movie extension.
Box Beam Backbone Sculptures
Design protein backbone sculptures made from metal box beams or wood. See also Gurnon, Voss-Andreae, and Stanley, PLoS Biol 11:e1001491 (2013).
Given a query structure, the server finds related sequences, aligns them, and displays conservation on the structure. Clicking the link to view results in Chimera uses the Chimera web data mechanism to display the structure and sequence alignment colored by conservation, as well as the ConSurf-calculated phylogenetic tree and custom alignment headers (example).
The server can compare two structures or search the PDB for structures similar to a query. The resulting pairwise superpositions can be viewed in Jmol and downloaded in various forms, including Chimera sessions.
Given 3D structures of molecules, DOCK addresses the problem of how they might fit or bind together. Using Chimera, one can:
For reconstructing 3d models from a set of randomly oriented particle images. EMAN includes the EMANimator extension for making animations in Chimera, focused on volume data.
The server searches the PDB for matches to a user-specified 3D motif (pattern of residues). The authors provide the Chimera extension ViewMatch for looking through the hits superimposed on the query. LabelHash can also be downloaded for local command-line use.
MoSuMo MoSuMo is a Semantic Web service for generating electrostatic potentials mapped to molecular surfaces. It requires the headless version of Chimera (Linux). MoSuMo can be downloaded from the Dumontier Lab, Carleton University, and is described in Gawronski and Dumontier, Comput Graph 35:823 (2011).
The Pfinder program predicts phosphate-binding sites in protein structures. It requires the headless version of Chimera (Linux). Pfinder can be downloaded from the Centre for Molecular Bioinformatics, University of Rome, and is described in Parca et al., Nucleic Acids Res 39:1231 (2011).
The Ringer program detects molecular motions by systematically sampling X-ray electron density; the aim is to go beyond static structural snapshots of proteins by uncovering structural ensembles. The program depends on Chimera. Ringer is available from the Alber lab at UC Berkeley, and is described in Lang et al., Protein Sci 19:1420 (2010).
Assignment of NMR spectra for determining protein and nucleic acid structures. Uses Chimera to display NMR peak assignments on a molecular model.
A plugin to Cytoscape that integrates visualization and analysis of protein networks or pathways in Cytoscape with visualization and analysis of corresponding structures in Chimera.
A Java plugin to Cytoscape that integrates 2D visualization of residue interaction networks (RINs) in Cytoscape with 3D visualization of corresponding structures in Chimera.
Given two protein conformations or an ID from the Database of Macromolecular Movements, the server generates a ViewMotions rainbow image and corresponding Chimera session. The conformational change is shown as a series of interpolated structures with variable regions rainbow-colored from blue to red. The server is described in Cockrell and Kantrowitz, J Mol Graph Model 40:48 (2013).
Computational Chemistry List (ccl.net)
PDB Discussion Forum (firstname.lastname@example.org)