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Web Services Used by UCSF Chimera

Web services accessed by Chimera fall into two general categories:

See also: Sites that provide Chimera web data

Data Retrieval Web Services Used by Chimera

ASTRAL Compendium
Allows fetching domain structures specified by SCOP domain identifier.

Computed Atlas of Surface Topography of proteins (CASTp)
Allows fetching precomputed pocket measurements and corresponding structures specified by PDB ID.

Electron Density Server (EDS)
Allows fetching electron density maps (2fo-fc and fo-fc) specified by PDB ID.

Electron Microscopy Data Bank (EMDB)
Allows fetching electron density maps by EMDB identifier and finding maps by keyword search.

ModBase
Allows fetching modeled structures (comparative models) specified by SwissProt, TrEMBL, GenPept or PIR accession code.

Nucleic Acid Database (NDB)
Translates NDB ID codes into PDB ID codes, which are then used to fetch structures from the PDB.

Protein Data Bank (RCSB PDB)
Allows fetching structures in PDB and mmCIF formats by PDB ID. Also provides lookup of other PDB entry information by Blast Protein and PDB/UniProt Info.

Protein Quaternary Structure (PQS)
Allows fetching predicted biological units specified by PDB ID.

PubChem3D
Allows fetching modeled organic molecule structures specified by PubChem CID.

UniProt
Allows fetching protein sequences and their feature annotations by UniProt ID, either for PDB structure chains by PDB/UniProt Info, or independent of structure.

Virus Particle Explorer database
Allows fetching icosahedral virus capsid structures (transformed into a standard orientation) specified by PDB ID.

Computational Web Services Used by Chimera

APBS
Chimera provides an interface to calculating electrostatic potential maps using an APBS (Adaptive Poisson-Boltzmann Solver) web service provided by the National Biomedical Computation Resource (NBCR).

AutoDock Vina
Chimera provides an interface to single-ligand docking calculations using an AutoDock Vina web service provided by the NBCR.

BLAST Protein
The Blast Protein tool performs protein sequence searches using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI).

Clustal Omega
Multiple sequence alignment with Clustal Omega can be performed using a web service hosted by the UCSF RBVI. The sequences of structure chains in Chimera can be submitted via the Align Chain Sequences tool, and/or sequences already in an alignment shown in Multalign Viewer can be submitted for realignment.

Modeller
Chimera provides an interface for comparative (homology) modeling, loop remodeling, and building missing segments using Modeller, either run locally or using a web service hosted by the UCSF RBVI.

MultiFit
The MultiFit tool performs simultaneous rigid fitting of multiple atomic-resolution structures into density maps using the program MultiFit (courtesy of Keren Lasker, Sali group) via a web service hosted by the UCSF RBVI.

MUSCLE
Multiple sequence alignment with MUSCLE can be performed using a web service hosted by the UCSF RBVI. The sequences of structure chains in Chimera can be submitted via the Align Chain Sequences tool, and/or sequences already in an alignment shown in Multalign Viewer can be submitted for realignment.

PDB2PQR
Chimera provides an interface to structure cleanup, parameter assignment, and PQR file generation using a PDB2PQR web service provided by the NBCR.

SaliLab Model Evaluation Server
Can be called to calculate additional scores for comparative models using the Fetch Scores menu in the Model List dialog.

Small-Angle X-Ray Profile
The Small-Angle X-Ray Profile tool calculates small-angle X-ray scattering (SAXS) profiles from structures using the program FoXS (courtesy of Dina Schneidman, Sali group) via a web service hosted by the UCSF RBVI.

SMILES Translator
The SMILES translator provided by the National Cancer Institute CADD group is used to generate 3D molecule structures specified by SMILES string with the command open or in Build Structure.

StrucTools
Used by Area/Volume from Web to calculate atomic surface areas (various methods) and Voronoi volumes from coordinates.

2D Chemical Diagram
Used by Structure Diagram and ViewDock to draw 2D diagrams of small organic molecules given coordinates or a SMILES string. This web service is implemented in Java using the Chemistry Development Kit and is provided by the UCSF RBVI.

Sites That Provide Chimera Web Data

Accessing Chimera web data (such as by clicking a link or choosing a display option at one of these sites) automatically displays database contents or server results in a locally installed copy of Chimera. See also: Web services used by Chimera

ConSurf Server
Clicking the link to view results in Chimera displays the query structure and the multiple sequence alignment from ConSurf, both colored by the server's conservation measure. The ConSurf-calculated phylogenetic tree and custom headers are shown along with the sequence alignment (see screenshot and details).

ModBase
The database contains predicted protein structures from comparative (homology) modeling. The “Chimera (Structure/Alignment)” option displays the modeled structure along with the template structure and the sequence alignment between the two. The “Visualize Surface Cavities (Chimera)” option shows a molecular surface of the modeled structure colored by ConCavity binding site prediction score.

MultiFit Webserver
The server performs simultaneous rigid fitting of multiple structures into a density map; clicking a thumbnail image in the results page opens the corresponding fitting solution in Chimera.

PhosphoSitePlus® (PSP)
Clicking “Get ChimeraX Script” on the Structure Viewer will show the structure in Chimera with experimentally observed sites of post-translational modification (PTM) colored and labeled. PSP is continuously updated with data on phosphorylation and other commonly studied PTMs.

SALIGN Webserver
The SALIGN server for multiple protein sequence/structure alignment can launch Chimera to display the superimposed structures and associated multiple sequence alignment.

Structure-Function Linkage Database
Chimera web data files are provided for viewing enzyme structures, active sites (Chimera sessions), and sequence alignments.

SwissDock Server
The SwissDock server allows launching Chimera (and its ViewDock tool) to display the results; the site includes a short example video.

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.