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
Famous quotes containing the words programming and/or dynamic:
“If there is a price to pay for the privilege of spending the early years of child rearing in the driver’s seat, it is our reluctance, our inability, to tolerate being demoted to the backseat. Spurred by our success in programming our children during the preschool years, we may find it difficult to forgo in later states the level of control that once afforded us so much satisfaction.”
—Melinda M. Marshall (20th century)
“The nearer a conception comes towards finality, the nearer does the dynamic relation, out of which this concept has arisen, draw to a close. To know is to lose.”
—D.H. (David Herbert)