What is MODELLER?
MODELLER is most frequently used for homology modeling of protein structure by satisfaction of spatial restraints 1:
The user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a model with all non-hydrogen atoms.
(Last updated: September | October 2017 – recompiled April 2019)
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.
- MODELLER I: Introduction. (same content, different formats)
- sequence files: blbp.fasta, 1HMS_A.fasta
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