MODELLER is used for homology or comparative modeling of protein three-dimensional structures. 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 the older MODELLER 9 software (any version from 9v4 through to 9.25). For modern MODELLER, see the regular MODELLER tutorial; for older versions of MODELLER, use the old MODELLER 7v7 tutorial. There are 5 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, ligands and loop refinement 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 difficult case of protein structure prediction.

  5. Modeling with cryo-EM. Model a sequence using both template and cryo-EM data.
    This exercise assesses the quality of generated models and loops by rigid fitting into cryo-EM maps, and improves them with flexible EM fitting.