Hi, I have some questions about fragment library used for de novo folding and loop modeling.
From what I have read, the score for ranking fragment conformations in a library consists of two parts, which are from psi-blast results and secondary structure prediction results. My questions are:
1) When performing the psi-blast that contributes to the ranking of fragment conformations in a library at one position, does the psi-blast involve the whole protein sequence or just a local region around that position?
2) If the query sequence doesn't have any homologs so that psi-blast doesn't work, how does the program rank fragment conformations? Is it then totally dependent on the secondary structure prediction?
3) The default size of fragment library at one position is 200. Does it mean in a de novo folding, all 200 conformations will be randomly selected with equal probability? And why in the Carol RoHl et al. METHODS IN ENZYMOLOGY (2004) paper, it says only the top 25 fragment conformations will be randomly selected?
Thanks a lot!!