AMBER Archive (2008)

Subject: AMBER: Question on AMBER MD Implications

From: Campbell, Patrick (pcampbell_at_msm.edu)
Date: Fri Oct 31 2008 - 11:27:41 CDT

Hello All,
 
I have a quick question concerning the implications of MD with AMBER.
 
I am aware of Anfinsen's dogma that the aa sequence can determine the folding pattern of a protein and also of Levinthal's paradox which states that for a polypeptide of length n amino acids, the possible number of folding possibilities is 4^n.
 
My question then is this - Is it reasonable to state that for a given protein subjected to MD, the number of low energy states that are derived during the simulation can give a relatively small set of possible aa folded states in contradiction to Levinthal's paradox?
 
I do look forward to your responses and have a great day!
 
Pat Campbell

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