Methods and Programs used by SWISS-MODEL

---

• Sequence Alignment:
  • BLAST:
    Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:403-410. (1990)

  • SIM:
    Huang, X., and Miller, M. A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12,337-367. (1991)

  • ProModII:
    Guex, N., and Peitsch, M.C. Structurally corrected multiple alignments.

  ---

• Comparative Protein Modelling:
  • ProMod / ProModII:
    Several publications.

  ---

• Energy Minimisation:
  • Gromos96:
    Information on this force field can be obtained from the ETH in Zürich.

  ---

• Model Evaluation:
  • Swiss-PdbViewer:
    Provides all necessary tools to evaluate the quality of a model. This feature is thus no longer provided by the SWISS-MODEL server.

---

Torsten Schwede , Manuel C. Peitsch & Nicolas Guex.