How does RAPTOR compare to MODELLER/MODELER?
They are complimentary products rather than replacements of each other. In short, they differ in the scale of their tasks. RAPTOR weeds out large amounts of unlikely proteins and indicates templates in the database that are closest in 3D shape to the query sequence. MODELLER/MODELER (or other comparative modelling tools) is specialized in modelling by “mapping” the query onto one template by satisfying spatial constraints. MODELLER/MODELER needs to know which template as the basis to build the model on, which is precisely what RAPTOR provides. It is keen at picking up similarities that might go undetected by other methods. MODELLER/MODELER is useful when the purpose of running RAPTOR is to get an accurate model based on templates from threading for possible structural analysis later. If, for example, only the query-template alignments are of interest, this step can be skipped. RAPTOR outputs in XML format. The module modellerProspect in the suite generates an alignment file from the XM
