RAPTOR is an innovative software designed for accurate protein structure prediction. It combines advanced analysis tools in one integrated software solution and provides three different threading methods. RAPTOR's unique integer programming optimization approach is most effective for finding structure templates of targets with low sequence homology and is able to generate high quality models. The easy-to-use interface and easy-to-understand E values are ideal for beginners and experts. Above all, the intuitive display of the output enables users to understand the results simply at a glance. Given a target protein sequence, if there is a homologous protein with known 3D structure, it can be found by using sequence search tools like PSI-BLAST, also provided in RAPTOR. The target's structure is then built from the known structure; however, when the sequence homology is not significant, i.e. less than 25%, PSI-BLAST can not come up with a confident hit. Unlike PSI-BLAST, which simply does a sequence search, protein threading, fold recognition, makes use of both homology and structure information. It scans the protein sequence with an unknown structure against a database of known structures. By using a scoring function and conducting compatibility analysis between three-dimensional structures and linear protein sequences, the best structural template will be identified from which to build the sequence's structure. As a result, protein threading gives a superior prediction than homology modeling when there is marginal sequence homology.
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