Template Based Techniques
As mentioned above homology-based methods use a database to align the target protein gap with a known template protein. A database of known structures is searched for a loop that fits the gap of interest by similarity of sequence and stems (the edges of the gap created by the unknown loop structure). The success of this method largely depends on the quality of that alignment. Since the loop is the least conserved portion of a protein’s structure, the homology-based method cannot always find a known template that aligns with the target sequence. Fortunately, the template databases are always adding new templates so the problem of not being able to find an alignment is becoming less of an issue. Some programs that use this method are SuperLooper and FREAD.
Read more about this topic: Loop Modeling
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