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.

Several views can be expanded using the buttons.

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.

If you are using models from the SWISS-MODEL Server or Repository, please cite the corresponding 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.
Kopp J, and Schwede T (2006). The SWISS-MODEL Repository: new features and functionalities. Nucleic Acids ResNucleic Acids Research 34, D315-D318.
Schwede, T., Kopp, J., Guex, N. and Peitsch, M.C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 31,3381-3385.
Arnold K, Bordoli L, Kopp J, and Schwede T (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics.,22,195-201.

The SWISS-MODEL Repository is providing cross links to the following servers and databases:

SCOP:
Lo Conte, L., Brenner, S.E., Hubbard, T.J.P., Chothia, C. and Murzin, A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.
CATH:
Orengo, C.A., Pearl, F.M.G., Bray, J.E., Todd, A.E., Martin, A.C., Lo, C.L. and Thornton, J.M. (1999) The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res., 27, 275-279.
InterPro:
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P. et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315-318.
ExPASy:
Gasteiger, E., Jung, E. and Bairoch, A. (2001) Swiss-Prot: connecting biological knowledge via a protein database. Curr. Issues Mol. Biol., 3, 47-55.
Swiss-Prot & TrEMBL:
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
NEWT:
http://www.ebi.ac.uk/newt/
Protein Data Bank PDB
Westbrook, J., Feng, Z., Chen, L., Yang, H. and Berman, H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489-491.

References to programs and algorithms mentioned or used at the SWISS-MODEL Server:

Gromos96:
van Gunsteren, W. (1996) Biomolecular Simulations: The GROMOS96 Manual and User Guide. VdF Hochschulverlag ETHZ.
ANOLEA:
Melo, F. and Feytmans, E. (1998) Assessing protein structures with a non-local atomic interaction energy. J. Mol. Biol., 277, 1141-1152.
AstexViewer2.0
Michael J. Hartshorn (2002) AstexViewer: A visualisation aid for structure-based drug design Journal of Computer Aided Molecular Design 16 , 871-881.
Rasmol:
Sayle, R.A. and Milner-White, E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
Jmol:
http://jmol.sourceforge.net
DINO:
http://www.dino3d.org
Molscript:
Per J. Kraulis (1991) MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures, Journal of Applied Crystallography 24, 946-950.
Raster3D:
Merritt, Ethan A. and Bacon, David J. (1997). Raster3D: Photorealistic Molecular Graphics, Methods in Enzymology 277, 505-524.
DeepView (Swiss-PdbViewer)
Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
BLAST & PSI-BLAST
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
SIM:
Huang, X., and Miller, M. (1991) A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12,337-367.
ProModII
Guex N and Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723.
EVA
Eyrich, V.A., Marti-Renom, M.A., Przybylski, D., Madhusudhan, M.S., Fiser, A., Pazos, F., Valencia, A., Sali, A. and Rost, B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243.

	SWISS-MODEL Documentation Workspace Tutorial Quick Help Protocol References Repository Quick Help References Structures & Models Visualisation Protein Structure Course SwissModel Helpdesk Repository Query by Sequence Query by AC Search by full text Tools Template Identification Domain Annotation Structure Assessment Template Library Modelling myWorkspace Automated Mode Alignment Mode Project Mode SWISS-MODEL Repository \| Help Introduction 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. Several views can be expanded using the buttons. *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. 1. Model Navigator 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. 2. Interpro Map 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. 3. Sequence Info 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. 4. Model Info 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. 5. Alignment 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 6. Anolea / Gromos Energy Plot 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.). 7. Modeling Log 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). 8. Template Selection Log 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. 9. Display and Visualization 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. 10. FAQ: How to link to the SWISS-MODEL Repository 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. 11. References *If you are using models from the SWISS-MODEL Server or Repository, please cite the corresponding 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. Kopp J, and Schwede T (2006). The SWISS-MODEL Repository: new features and functionalities. Nucleic Acids ResNucleic Acids Research 34, D315-D318. Schwede, T., Kopp, J., Guex, N. and Peitsch, M.C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 31,3381-3385. Arnold K, Bordoli L, Kopp J, and Schwede T (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics.,22,195-201. *The SWISS-MODEL Repository* is providing cross links to the following servers and databases: SCOP: Lo Conte, L., Brenner, S.E., Hubbard, T.J.P., Chothia, C. and Murzin, A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267. CATH: Orengo, C.A., Pearl, F.M.G., Bray, J.E., Todd, A.E., Martin, A.C., Lo, C.L. and Thornton, J.M. (1999) The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res., 27, 275-279. InterPro: Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P. et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315-318. ExPASy: Gasteiger, E., Jung, E. and Bairoch, A. (2001) Swiss-Prot: connecting biological knowledge via a protein database. Curr. Issues Mol. Biol., 3, 47-55. Swiss-Prot & TrEMBL: Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370. NEWT: http://www.ebi.ac.uk/newt/ Protein Data Bank PDB Westbrook, J., Feng, Z., Chen, L., Yang, H. and Berman, H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489-491. References to programs and algorithms mentioned or used at the SWISS-MODEL Server: Gromos96: van Gunsteren, W. (1996) Biomolecular Simulations: The GROMOS96 Manual and User Guide. VdF Hochschulverlag ETHZ. ANOLEA: Melo, F. and Feytmans, E. (1998) Assessing protein structures with a non-local atomic interaction energy. J. Mol. Biol., 277, 1141-1152. AstexViewer2.0** Michael J. Hartshorn (2002) AstexViewer: A visualisation aid for structure-based drug design Journal of Computer Aided Molecular Design 16 , 871-881. Rasmol: Sayle, R.A. and Milner-White, E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374. Jmol: http://jmol.sourceforge.net DINO: http://www.dino3d.org Molscript: Per J. Kraulis (1991) MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures, Journal of Applied Crystallography 24, 946-950. Raster3D: Merritt, Ethan A. and Bacon, David J. (1997). Raster3D: Photorealistic Molecular Graphics, Methods in Enzymology 277, 505-524. DeepView (Swiss-PdbViewer) Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723. BLAST & PSI-BLAST Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. SIM: Huang, X., and Miller, M. (1991) A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12,337-367. ProModII Guex N and Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723. EVA Eyrich, V.A., Marti-Renom, M.A., Przybylski, D., Madhusudhan, M.S., Fiser, A., Pazos, F., Valencia, A., Sali, A. and Rost, B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243.
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