Tutorial

MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2,3). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.

This web site presents a tutorial for the use of MODELLER 7v7 (the examples should, however, work with other versions of MODELLER with minor modifications; Python input files for MODELLER 8v0 are also provided in the downloadable .zip or .tar.gz archives). There are 4 modeling examples that the user can follow:

1. Basic Modeling. Model a sequence with high identity to a template.
   This exercise introduces the use of MODELLER in a simple case where the template selection and target-template alignments are not a problem.

2. Advanced Modeling. Model a sequence based on multiple templates and bound to a ligand.
   This exercise introduces the use of multiple templates and ligands in the process of model building with MODELLER.

3. Iterative Modeling. Increase the accuracy of the modeling exercise by iterating the 4 step process.
   This exercise introduces the concept of MOULDING to improve the accuracy of comparative models.

4. Difficult Modeling. Model a sequence based on a low identity to a template.
   This exercise uses resources external to MODELLER in order to select a template for a dificult case of protein structure prediction.

1. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.

2. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

3. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.