text: user9890: 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?
  
  user4622: 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 >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.
  
original_text: 9890: <p>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?</p>
   4622: <p>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).</p>
  <p>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.</p>
  <p>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.</p>
  