Twelve homology models of the human M2 muscarinic receptor using different sets 
of templates have been designed using the Prime program or the modeller program 
and compared to crystallographic structure (PDB:3UON). The best models were 
obtained using single template of the closest published structure, the M3 
muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led 
to worse models. Data document a key role of the template in homology modeling. 
The models differ substantially. The quality checks built into the programs do 
not correlate with the RMSDs to the crystallographic structure and cannot be 
used to select the best model. Re-docking of the antagonists present in 
crystallographic structure and relative binding energy estimation by calculating 
MM/GBSA in Prime and the binding energy function in YASARA suggested it could be 
possible to evaluate the quality of the orthosteric binding site based on the 
prediction of relative binding energies. Although estimation of relative binding 
energies distinguishes between relatively good and bad models it does not 
indicate the best one. On the other hand, visual inspection of the models for 
known features and knowledge-based analysis of the intramolecular interactions 
allows an experimenter to select overall best models manually.