Fundamentally, the electron cloud distribution is [maybe] represented by
Schrondinger's equation. For a more molecule more complicated than
hydrogen, this is an unsolved problem. To think that one can just throw
enough computational horsepower at a spring mass type problem will yield
correct results is wrong.
A joke comes to mind that a friend told me. A guy was walking down the
street when he ran across another passerby who was on his hands and knees
looking for something on the ground.
First man says, "What are you looking for?"
Second man says, "My bus change."
First man says, "Oh where did you loose it".
Second man says, "Back in the alley."
First man says, "Then, why are you looking here on the street corner"
Second man says, "Because, the street lamp is here."
All the CPU throughput won't help if you don't first solve the mathematics
correctly. I studied mathematics and numerical analysis and have obtained a
M. Sc, so I have somewhat of an understanding of the problems involved. I
learned about differential equations and difference equation. A simple 2nd
order differential equation is approximated by a third order difference
equation. A fundamental theorem says that a 2nd order differential equation
has 2 characteristic equation, while a 3rd order difference equation has 3
characteristic equations. Hence, there will be solutions to the second
equation which are not solutions to original problem. These are called
"parasitic solutions." Yes, there are ways to deal with those, however, you
would be lucky if that's all that is wrong. The problems are usually much
more severe.
I am trying to understand how to tackle this protein folding problem.
Does anyone know of any good resources about how to solve the problem from
first principles. I have read people's papers on methods based on
sophisticated computational dynamics, but those avoid the approach I was
looking for.
-Deodiaus
Louis Hom wrote in message <93i4fe$c06$1 at agate.berkeley.edu>...
>In article <3A5BC1BB.4663055 at home.com>, bjhenry1 <bjhenry1 at home.com>
wrote:
> These are fairly basic calculations, but there are a lot of
>them -- a lot of them for each possible structure (folded or misfolded)
>that we want to assess. And if you are start with a random coil of your
>protein and you want to figure out its final structure, you're going to
>have to consider a lot of different structures (right and wrong) along the