SWISS-MODEL Repository References

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

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 is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.