Integer Programming Vs. Dynamic Programming
The integer programming approach to RAPTOR produces higher quality models than other protein threading methods. Most threading software use dynamic programming to optimize their scoring functions when aligning a sequence with a template. Dynamic programming is much easier to implement than integer programming; however if a scoring function has pairwise contact potential included, dynamic programming cannot globally optimize such a scoring function and instead just generates a local optimal alignment.
Pairwise contacts are very conserved in protein structure and crucial for prediction accuracy. Integer programming can globally optimize a scoring function with pairwise contact potential and produce a global optimal alignment.
Read more about this topic: RAPTOR (software), Comparison of Techniques
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