This section contains three examples of a typical comparative modeling application. All the examples use program MODELLER-6 and other freely available software. The first example demonstrates each of the five steps of comparative modeling at their most basic level. The second example illustrates the use of multiple templates and modeling of a protein with a ligand and a co-factor, as well as applying user-defined restraints for docking a substrate molecule into the active site pocket. In the third example, we describe a loop modeling exercise. All the input and output files for MODELLER-6 can be downloaded from http://guitar.rockefeller.edu/modeller/methenz/. For more information, the MODELLER manual  and literature [22,23,43,44,24] can be consulted. A list of our papers using MODELLER to address practical problems in collaboration with experimentalists can be obtained at URL http://guitar.rockefeller.edu/modeller/methenz/.
Although the main purpose of MODELLER is model building, it can be used in all stages of comparative modeling, including template search, template selection, target-template alignment, model building, and model assessment. Once a target-template alignment is obtained, the calculation of a 3D model of the target by MODELLER is completely automated.