SWISS-MODEL

The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. The repository is developed at the Biozentrum Basel within the Swiss Institute of Bioinformatics.

The repository currently contains three-dimensional models for sequences from the UniProt knowledge base. The content of the repository is updated on a regular basis incorporating new sequences, taking advantage of new template structures becoming available, and reflecting improvements in the underlying modelling algorithms. The current data status is given on the entry page.

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009). The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.

The "model navigator" provides an overview of the models (blue bars, dark blue >70% sequence identity ,light blue <70% sequence identity) that have been generated for the given UniProt target sequence (green bar). A red border indicates the selected model,if more than one model for this sequence is in the Repository. Click on a model bar to select a model.

The Interpro Map shows a graphical overview of the InterPro matches to the target sequence. Only hits flagged as "true" are included in this representation.The underlying link leads to the detailed page for this entry at InterPro.

The sequence info view provides information about the sequence origin and taxonomic classification extracted from Swiss-Prot. Links are provided to its original Swiss-Prot entry, NEWT taxonomy browser and domain assignment in InterPro.

A small ribbon representation is generated (using Molscript and Raster3D) to get a first impression of the model. Clicking on the small image or "display in browser" starts the AstexViewer applet and loads the selected model. Model coordinates can be downloaded in PDB format, as plain text or as DeepView projects. See: Visualization.

The target-template alignment provides additionally the assignment of the secondary structure elements of the target structure and the model ("s" for strand and "h" for helical region):

   Model     1       KSCCPSIT ARNTYNVCRL PGTPRPVCAS ISGCKILSVT KCPSNLP   
   Template          KSCCPNTT GRNIYNACRL TGAPRPTCAK LSGCKIISGS TCPSDYPK  
                     *****. * .** ** ***  *.*** **  .*****.* .  ***. *   
   Model             sss   hh hhhhhhhhh      hhhhhh hh  sss              
   Template          sss   hh hhhhhhhhhh     hhhhhh hh  sss              

Force Field energies have been calculated using a partial implementation of Gromos96 (van Gunsteren et al.). The atomic empirical mean force potential ANOLEA is used to assess packing quality of the models (Melo et al.).

The models have been built using a modified version of the automated SWISS-MODEL server pipeline (Schwede et al.). The modelling log shows the individual steps performed by the ProModII program during model building (Guex et al.), especially which parts of the model have been built ab initio (i.e. insertions / deletions).

The template selection log file provides information about the template selection step using BLAST (Altschul et al.) and HHSearch (Soding) to search the SWISS-MODEL template library for suitable templates. For each template structure a link to the SWISS-MODEL template library is given.

Clicking on the small ribbon image or "display in browser" starts the AstexViewer2.0 applet and loads the selected model.

The SWISS-MODEL Repository provides access to the model coordinates in two different formats: DeepView project files (recommended) and PDB format.

DeepView project files contain the final model, superposed to the template structure. The program DeepView allows to visualize the model and the templates, and to analyse certain structural features e.g. Ramachandran plots or electrostatic properties. Moreover, it allows adjusting manually the placement of insertions and deletions in the alignment on which the initial modelling process was based on. The project with the modified alignment can then be re-submitted to the SWISS-MODEL server for model building.

DeepView (Swiss-PdbViewer)is a powerful program with a user-friendly interface that is available for Windows PC and Mac. DeepView can be downloaded for free at:

http://www.expasy.org/spdbv/

DeepView does not require administrator privileges for installation. E.g. under MS windows, simply uncompress the distributed archive at any location you like (e.g. c:\spdbv or on your desktop) and start working by starting the spdbv.exe application.

PDB formatted protein models can be displayed by any molecular visualization tool or browser-plugin. Here is a short list of freely available software:

• DeepView (MS Windows, Macintosh)
• DINO (Linux, IRIX, OSF,SUN)
• Rasmol (MS Windows, Mac, Unix)
• CHIME Plugin (requires registration)

Linking mime-types and viewer applications:

When using the "Display" links of the SWISS-MODEL Repository web site, the model coordinates will be sent back to you browser with the Mime-Type "chemical/pdb" for PDB formatted files, and "chemical/x-spdbv" for DeepView project files.

• Can I put a link to the SWISS-MODEL Repository on my web site?
  
  Yes, please. To set a link to the SWISS-MODEL Repository on your web site, please use the following URL:
  
  http://swissmodel.expasy.org/repository/
  
  
• Can I create a link directly to a specific Swiss-Prot or trEMBL entries in the SWISS-MODEL Repository?
  
  Individual Swiss-Prot or trEMBL entries in the repository can be linked using Swiss-Prot / trEMBL accession codes. Please make sure that you are using ONLY accession codes (e.g. P01543) and no other identifiers (like gene names, genbank ac codes, etc.)
  
  http://swissmodel.expasy.org/repository/smr.php?sptr_ac=AC_CODE
  
• Can I create a link directly to a specific model file in the SWISS-MODEL Repository?
  
  No. It is not a good idea to create links to specific model files in the SWISS-MODEL Repository, because these entries are likely to change between updates of the database.
  
  
• Can I use the model image thumbnails from the SWISS-MODEL Repository in my own web page?
  
  No. These images are generated dynamically for SWISS-MODEL Repository web site using Molscript and Raster3D. They should not be used in any other context.
  
  
• Can I download the whole SWISS-MODEL Repository and store it locally.
  
  No. Please don't try this.

It has been shown that there is a direct correlation between the sequence identity level of a pair of protein structures and the deviation of the Cα atoms of their common core (Chothia, C. & Lesk, EMBO J. 5, 823–826 (1986)). The more similar two sequences are, the closer the corresponding structures can be expected to be and the larger the fraction of the model that can be directly inferred from the template. As comparative models result from a structural extrapolation guided by a sequence alignment, the percentage of sequence identity between target and template is generally accepted as a reasonable first estimate of the quality of the structurally conserved core of the model.

In SWISS-MODEL Repository, the quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. Currently our method is limited to the modeling of homo-oligomeric assemblies, where the sequence identity between target and template sequences is higher than 60%.

In SWISS-MODEL Repository modeling of essential metal ions and cofactors include a ligand to the modeled target sequence by comparing the template's binding site residues with the corresponding ones in the target sequence.