Simple demonstrations of MODELLER in all steps of comparative protein structure modeling, including fold assignment, sequence-structure alignment, model building, and model assessment, can be found in references listed at http://salilab.org/modeller/documentation.html. A number of additional tools useful in comparative modeling are listed at http://salilab.org/bioinformatics_resources.shtml. Specifically, users have access to MODBASE, a comprehensive database of comparative models for all known protein sequences detectably related to at least one known protein structure; MODWEB, a web server for automated comparative protein structure modeling; and MODLOOP, a web server for automated modeling of loops in protein structures. For ``frequently-asked-questions'' (FAQ), see Section 3.1.
The rest of this section is a `hands on' description of the most basic use of MODELLER in comparative modeling, in which the input are Protein Data Bank (PDB) atom files of known protein structures, and their alignment with the target sequence to be modeled, and the output is a model for the target that includes all non-hydrogen atoms. Although MODELLER can find template structures as well as calculate sequence and structure alignments, it is better in the difficult cases to identify the templates and prepare the alignment carefully by other means. The alignment can also contain very short segments such as loops, secondary structure motifs, etc.