Questions about rosetta fragment library ranking and fragment conformation sampling algorithm
Submitted by mdyini on Thu, 2011-05-19 17:34
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?
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