Homology modeling process.



(Last updated: September | October 2017 – recompiled April 2019)

Tutorial 1:

The MODELLER software is a set of python scripts and all steps can be accomplished via line-command: this is what is explored in the first tutorial.

Tutorial 2:

The graphical interface of Chimera can be used to run MODELLER

  • MODELLER II:  Chimera GUI interface. (same content, different formats)


  • Šali, A. & Blundell, T. L. (1993). “Comparative Protein Modelling by Satisfaction of Spacial Restraints.” J. Mol. Biol. 234, 779-815.DOI:10.1006/jmbi.1993.1626, Pubmed: 8254673,  PDF.
  • Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. “UCSF Chimera – A Visualization System for Exploratory Research and Analysis.” J. Comput. Chem. 25:1605-1612 (2004). Pubmed: 15264254. DOI:10.1002/jcc.20084

  1. https://salilab.org/modeller/9.19/manual/node7.html