This section is a `hands on' description of the most basic use of MODELLER in comparative modeling. For an outline of the main stages in comparative modeling, see Section 1.7. For ``frequently-asked-questions'' (FAQ), see Section 1.9. An introductory, hands-on primer to comparative modeling with several MODELLER examples can be found in SanSalRev98.
The input are Protein Data Bank (PDB) atom files of known protein structures and their alignment with the target sequence to be modeled. The output is a model for the target that includes all non-hydrogen atoms. Although MODELLER can calculate sequence and structure alignments, it is better to prepare the alignment carefully by other means. The alignment can also contain very short segments such as loops, secondary structure motifs, etc.
This tutorial assumes that MODELLER is already installed on your computer and that appropriate changes have been made to your login script to install you as a MODELLER user. See Section 1.4 for more details on installation (also in the INSTALLATION file in the MODELLER distribution directory).