Chimera-Related Databases and Software

See also: Web services used by UCSF Chimera, sites that provide Chimera Web data, and Chimera plug-ins on the Web

Databases

ASTRAL
Experimentally determined protein structures, divided into domains as defined by SCOP (Structural Classification of Proteins).

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).

Database 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).

Electron Density Server at PDBe

Crystallographic electron density maps for Protein Data Bank x-ray structures. Display density maps with Chimera Volume Viewer.

EM DataBank (EMDB)

This site contains 3D density maps obtained by electron microscopy in CCP4 format that can be shown with Chimera Volume Viewer.

EM Navigator
Presents images, movies, Chimera sessions and details about electron microscopy density maps from the EM DataBank.

LS-SNP/PDB
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.

ModBase
A database of three-dimensional protein models calculated by comparative modeling. The website includes links for viewing models in Chimera along with the corresponding template structure and template-target sequence alignment, or colored to show binding site predictions. ModBase models and associated information can also be fetched directly into Chimera.

Mutagenetix
A database of mouse mutations and phenotypes induced by ENU. Many of the allele pages include molecular structure images and movies made in Chimera (example).

PhosphoSitePlus®

Comprehensive information and tools for the study of protein post-translational modifications; includes scripts for visualization in Chimera.

RCSB Protein Data Bank (PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj)
Experimentally determined protein and nucleic acid structures. Display PDB and mmCIF format files of atomic coordinates.

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.

Virus Particle Explorer

Atomic resolution virus capsid structures. Some of the capsid images on this site are made with the Chimera Multiscale Models tool.

Software

AlphaSpace

AlphaSpace is a tool for analyzing surface pockets at protein-protein interfaces. AlphaSpace generates a Chimera session file with several “scenes” for viewing the results in different ways. The program is available upon request from the authors for academic use and is described in Rooklin et al., J Chem Inf Model 55:1585 (2015).

Amber
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). The new user interface was developed by Evan Zelesnik while the old user interface was made by Tom Goddard.

CanDo Atomic Model Generator
Uses Chimera to generate atomic models of DNA nanostructures from the description in the CanDo (.cndo) file format. Chimera is also used to generate 3D printable models from CanDo.

cellPACK
cellPACK is a tool for assembling large-scale models from molecular building blocks; it integrates structural biology and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. Chimera can be used to view and analyze cellPACK models.

ConEVA Server
Given file(s) of predicted contacts, the ConEVA (contact evaluation) server provides several methods for visualizing and comparing them, with or without associated structures. If a structure is available, results include Chimera scripts for 3D visualization. Several example data sets are available on the website. The server is described in Adhikari et al., BMC Bioinformatics 17:517 (2016).

ConSurf Server

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).

deconSTRUCT Server
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.

Direct Coupling Analysis

Direct Coupling Analysis (DCA) is a statistical inference framework for identifying direct co-evolutionary couplings among residue pairs in multiple sequence alignments. A protein multiple sequence alignment can be uploaded to the web service, or the code can be downloaded for local use. The download includes a Matlab implementation and scripts for 3D visualization in Chimera as described in Morcos et al., Methods Mol Biol 1137:55 (2014).

DOCK
Given 3D structures of molecules, DOCK addresses the problem of how they might fit or bind together. Using Chimera, one can:

EMAN2 – Electron Micrograph Analysis

Image processing suite for single-particle reconstruction from cryo-EM and working with data from related subdisciplines such as tomography and 2D crystallography. The previous program EMAN1 included the EMANimator extension for making volume-data (map) animations in Chimera.

JEvTrace
JEvTrace is a Java implementation of the evolutionary trace method. Results can be shown in Chimera as coloring of the sequence alignment and any associated structures by reading a JEvTrace output file into Multalign Viewer.

LabelHash Server
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.

MacroMoleculeBuilder (MMB)
MMB is a multiresolution modeling tool for building 3D structural and dynamical models of macromolecules, with explicit control over degrees of freedom, forces, and constraints; it was previously known as RNABuilder but now also handles protein and DNA. MMB is available for download along with a plugin for using Chimera as the GUI, as described in Tek et al., Nucleic Acids Res 44:95 (2016).

Partial Order Structure Alignment (POSA) Server

The POSA server performs flexible multiple structure alignment. The results visualization page includes a link to download a python script for viewing the superimposed structures in Chimera. The POSA server is described in Li et al., Nucleic Acids Res 42:W240 (2014).

ResMap
ResMap (Resolution Map) is a Python application for computing the local resolution of cryo-EM density maps. It generates a map of the local resolution and a Chimera script for 3D visualization. ResMap is available on SourceForge and described in Kucukelbir et al., Nature Methods 11:63 (2014). See also: LocalFSC

Ringer

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 for download and is described in Lang et al., Protein Sci 19:1420 (2010).

SketchBio
A tool for molecular modeling and animation that uses Chimera for surface generation.

Sparky
Assignment of NMR spectra for determining protein and nucleic acid structures. Uses Chimera to display NMR peak assignments on a molecular model.

structureViz2

A Cytoscape app that integrates protein networks or pathways in Cytoscape with visualization and analysis of corresponding structures in Chimera. It also works with RINalyzer to calculate residue interaction networks (RINs) for Cytoscape from protein structures in Chimera.


ViewMotions Server

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).

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