How do you calculate the top L/5 score? I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do you use to evaluate these? Also, what is a meaningful evaluation method?
A contact map predictor will usually output the probability of a contact for every residue pair in a protein, often ommitting very close pairs (e.g. less than 6 residue separation).
To calculate the L/n score, rank the predicted contacts descending by probability and look at the first L/n contacts. The fraction of these that are actually contacts in the native structure is the L/n contact precision score.
Often, you would filter the list to look at only contacts of a certain sequence separation, e.g. long range contacts between residues of &gt;23 separation (definitions vary between papers). If you have a good predictor this score is high for L/10 and falls as you go to L/1, which is expected as proteins don't usually have that many long range contacts to find.