Cluster algorithm, discussion

The first stage of our prediction algorithm applies the MCM-based approach described above to each of the nine secondary structure predictions for each target. Simulations are usually carried out on two to four nodes of a multiprocessor machine and take between 12 and 24 hours depending on protein size. To extract the structurally unique predictions, we apply the clustering algorithm discussed above. Table VIII shows the results of this procedure for the three targets discussed in more detail below. We list results for every secondary structure prediction (unless predictions consist only of loop or cod, in which case we did not believe it worthwhile to carry out the simulation). 

Classification of hits into different phenotype classes is a debated issue in the field. Many clustering algorithms are implemented in KNIME and a discussion about the choice of algorithm to use goes beyond the scope of this chapter. However, a clustering approach... 

The authors would like to thank Eytan Domany, Jon Machta and Alan Sokal for useful discussions about cluster algorithms, and Daniel Kandel for supplying a copy of his Ph.D. thesis. 

---