Author: Miguel A. Ballicora
Date: 19:24:45 08/05/02
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On August 05, 2002 at 18:13:33, Dieter Buerssner wrote: >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 Sorry, I misused the O() notation, my mistake. I was talking about iterations. A liner regression takes 1 iteration or cycle. The more linear the parameters behave, the less iterations you need, even for approximations (those do not need to be O(n^3)). Regards, Miguel >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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