SWISS-MODEL

SWISS-MODEL Workspace References

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

SWISS-MODEL Workspace:

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.

Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J. and Schwede, T. (2009). Protein structure homology modelling using SWISS-MODEL Workspace. Nature Protocols, 4,1.
SWISS-MODEL Repository:

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.
SWISS-MODEL Server:

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.
SWISS-MODEL and Swiss PdbViewer

Guex N and Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723.

The SWISS-MODEL Workspace 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:

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.
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.
SCOP
Andreeva, A., D. Howorth, et al. (2004). "SCOP database in 2004: refinements integrate structure and sequence family data." Nucleic Acids Res 32(Database issue): D226-9.
UniProt
Bairoch, A., R. Apweiler, et al. (2005). "The Universal Protein Resource (UniProt)." Nucleic Acids Res 33 Database Issue: D154-159.
Verify3D
Eisenberg, D., R. Luthy, et al. (1997). "VERIFY3D: assessment of protein models with three-dimensional profiles." Methods Enzymol 277: 396-404.
DeepView (Swiss-PdbViewer)
Guex, N. and M. C. Peitsch (1997). "SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling." Electrophoresis 18(15): 2714-2723.
WhatCheck
Hooft, R. W., G. Vriend, et al. (1996). "Errors in protein structures." Nature 381(6580): 272.
Promotif
Hutchinson, E. G. and J. M. Thornton (1996). "PROMOTIF - - a program to identify and analyze structural motifs in proteins." Protein Sci 5(2): 212-20.
PsiPred
Jones, D. T. (1999). "Protein secondary structure prediction based on position-specific scoring matrices." J Mol Biol 292(2): 195-202.
Disopred
Jones, D. T. and J. J. Ward (2003). "Prediction of disordered regions in proteins from position specific score matrices." Proteins 53 Suppl 6: 573-578.
MEMSAT
Jones, D.T. , Taylor, W.R. & Thornton, J.M. "A model recognition approach to the prediction of all-helical membrane protein structure and topology." Biochemistry 33, 3038-3049
DSSP
Kabsch, W. and C. Sander (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features." Biopolymers 22: 2577-2637.
HHsearch
Söding J. (2005) "Protein homology detection by HMM-HMM comparison." Bioinformatics 21, 951-960. doi:10.1093/bioinformatics/bti125.
Procheck
Laskowski R A, Chistyakov V V, Thornton J M (2005). PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33, D266-D268.
PDBsum
Laskowski, R. A., V. V. Chistyakov, et al. (2005). "PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids." Nucleic Acids Res 33(Database issue): D266-268
CDHIT
Li, W., L. Jaroszewski, et al. (2002). "Sequence clustering strategies improve remote homology recognitions while reducing search times." Protein Eng 15(8): 643-649.
Anolea
Melo, F. and E. Feytmans (1998). "Assessing protein structures with a non-local atomic interaction energy." J Mol Biol 277(5): 1141-1152.
DFIRE
Zhou, H., and Zhou, Y. (2002). "Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. " Protein Sci. 11:2714-2726.
QEMAN
Benkert, P., Tosatto, S.C.E. and Schomburg, D. (2008). "QMEAN: A comprehensive scoring function for model quality assessment. " Proteins: Structure, Function, and Bioinformatics, 71(1):261-277.
InterPro
Mulder, N. J., R. Apweiler, et al. (2005). "InterPro, progress and status in 2005." Nucleic Acids Res 33 Database Issue: D201-205.
CATH
Pearl, F., A. Todd, et al. (2005). "The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis." Nucleic Acids Res 33 Database Issue: D247-51.
SWISS-MODEL
Schwede, T., J. Kopp, et al. (2003). "SWISS-MODEL: An automated protein homology-modeling server." Nucleic Acids Res 31(13): 3381-3385.
Gromos
van Gunsteren, W. F., S. R. Billeter, et al. (1996). Biomolecular Simulations: The GROMOS96 Manual and User Guide. Zürich, VdF Hochschulverlag ETHZ.
PQS
Henrick K, Thornton JM, PQS: "A protein quarternary file server." Trends Biochem. Sci. 1998;23:358-361.
PDBe
Velankar, S., P. McNeil, et al. (2005). "E-MSD: an integrated data resource for bioinformatics." Nucleic Acids Res 33 Database Issue: D262-265.
PDB RCSB
Westbrook, J., Z. Feng, et al. (2003). "The Protein Data Bank and structural genomics." Nucleic Acids Res 31(1): 489-491.
NR
Wheeler, D. L., T. Barrett, et al. (2005). "Database resources of the National Center for Biotechnology Information." Nucleic Acids Res 33 Database Issue: D39-45.
IPRscan
Zdobnov, E. M. and R. Apweiler (2001). "InterProScan - an integration platform for the signature-recognition methods in InterPro." Bioinformatics 17(9): 847-848.

	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 Workspace References *If you are using models from the SWISS-MODEL Server or Repository, please cite the corresponding articles:* SWISS-MODEL Workspace: 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. Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J. and Schwede, T. (2009). Protein structure homology modelling using SWISS-MODEL Workspace. Nature Protocols, 4,1. SWISS-MODEL Repository: 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. SWISS-MODEL Server: 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. SWISS-MODEL and Swiss PdbViewer Guex N and Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723. *The SWISS-MODEL Workspace* 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: 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. 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. SCOP Andreeva, A., D. Howorth, et al. (2004). "SCOP database in 2004: refinements integrate structure and sequence family data." Nucleic Acids Res 32(Database issue): D226-9. UniProt Bairoch, A., R. Apweiler, et al. (2005). "The Universal Protein Resource (UniProt)." Nucleic Acids Res 33 Database Issue: D154-159. Verify3D Eisenberg, D., R. Luthy, et al. (1997). "VERIFY3D: assessment of protein models with three-dimensional profiles." Methods Enzymol 277: 396-404. DeepView (Swiss-PdbViewer) Guex, N. and M. C. Peitsch (1997). "SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling." Electrophoresis 18(15): 2714-2723. WhatCheck Hooft, R. W., G. Vriend, et al. (1996). "Errors in protein structures." Nature 381(6580): 272. Promotif Hutchinson, E. G. and J. M. Thornton (1996). "PROMOTIF - - a program to identify and analyze structural motifs in proteins." Protein Sci 5(2): 212-20. PsiPred Jones, D. T. (1999). "Protein secondary structure prediction based on position-specific scoring matrices." J Mol Biol 292(2): 195-202. Disopred Jones, D. T. and J. J. Ward (2003). "Prediction of disordered regions in proteins from position specific score matrices." Proteins 53 Suppl 6: 573-578. MEMSAT Jones, D.T. , Taylor, W.R. & Thornton, J.M. "A model recognition approach to the prediction of all-helical membrane protein structure and topology." Biochemistry 33, 3038-3049 DSSP Kabsch, W. and C. Sander (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features." Biopolymers 22: 2577-2637. HHsearch Söding J. (2005) "Protein homology detection by HMM-HMM comparison." Bioinformatics 21, 951-960. doi:10.1093/bioinformatics/bti125. Procheck Laskowski R A, Chistyakov V V, Thornton J M (2005). PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33, D266-D268. PDBsum Laskowski, R. A., V. V. Chistyakov, et al. (2005). "PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids." Nucleic Acids Res 33(Database issue): D266-268 CDHIT Li, W., L. Jaroszewski, et al. (2002). "Sequence clustering strategies improve remote homology recognitions while reducing search times." Protein Eng 15(8): 643-649. Anolea Melo, F. and E. Feytmans (1998). "Assessing protein structures with a non-local atomic interaction energy." J Mol Biol 277(5): 1141-1152. DFIRE Zhou, H., and Zhou, Y. (2002). "Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. " Protein Sci. 11:2714-2726. QEMAN Benkert, P., Tosatto, S.C.E. and Schomburg, D. (2008). "QMEAN: A comprehensive scoring function for model quality assessment. " Proteins: Structure, Function, and Bioinformatics, 71(1):261-277. InterPro Mulder, N. J., R. Apweiler, et al. (2005). "InterPro, progress and status in 2005." Nucleic Acids Res 33 Database Issue: D201-205. CATH Pearl, F., A. Todd, et al. (2005). "The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis." Nucleic Acids Res 33 Database Issue: D247-51. SWISS-MODEL Schwede, T., J. Kopp, et al. (2003). "SWISS-MODEL: An automated protein homology-modeling server." Nucleic Acids Res 31(13): 3381-3385. Gromos van Gunsteren, W. F., S. R. Billeter, et al. (1996). Biomolecular Simulations: The GROMOS96 Manual and User Guide. Zürich, VdF Hochschulverlag ETHZ. PQS Henrick K, Thornton JM, PQS: "A protein quarternary file server." Trends Biochem. Sci. 1998;23:358-361. PDBe Velankar, S., P. McNeil, et al. (2005). "E-MSD: an integrated data resource for bioinformatics." Nucleic Acids Res 33 Database Issue: D262-265. PDB RCSB Westbrook, J., Z. Feng, et al. (2003). "The Protein Data Bank and structural genomics." Nucleic Acids Res 31(1): 489-491. NR Wheeler, D. L., T. Barrett, et al. (2005). "Database resources of the National Center for Biotechnology Information." Nucleic Acids Res 33 Database Issue: D39-45. IPRscan Zdobnov, E. M. and R. Apweiler (2001). "InterProScan - an integration platform for the signature-recognition methods in InterPro." Bioinformatics 17(9): 847-848.
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