 To address the problem of inaccuracies in initial target-template sequence alignment, an iterative procedure has also been introduced to refine the alignment on the basis of the initial structural fit.The most commonly used software in spatial restraint-based modeling is MODELLER and a database called ModBase has been established for reliable models generated with it.Regions of the target sequence that are not aligned to a template are modeled by loop modeling; they are the most susceptible to major modeling errors and occur with higher frequency when the target and template have low sequence identity.