Author: Dieter Buerssner
Date: 15:13:33 08/05/02
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On August 04, 2002 at 15:43:49, Miguel A. Ballicora wrote: >5000 parameters is not much when compared to the parameters needed to obtain the >optimal conformation of a protein with a computer. In that case, it is almost >impossible (with the current knowledge) to obtain the right conformation >starting from scratch, but is is very doable when you start from the "optimal" >conformation (determine by physical methods, not by a computer), you change >something and see how the new conformation would look like. Iterations around >the minimum are very fast because all the parameters behave almost linearly or >close enough. When the parameters behave linearly the time to resolve the >problem is O(1) (a linear regresion of n parameters is O(1)). Miguel, I cannot follow here. It is some time ago, but I studied many multi-parameter optimization methods. My memory tells me, that for linear regression (the easiest case - not?) this involves solving a linear system of n equations. This would be O(n^3) - certainly not a trivial task for n=5000, besides all the (serious) numerical instabilities, one could await for this task - especially when trying to solve it in a rather straightforward manner. Regards, Dieter
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