"deodiaus" <deodiausNOSPAM at gnu.ai.mitNOSPAM.edu> wrote:
: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.
The problem, as I see it, is compounded by the fact that many
protein folds (probably most? - famous RNAse seems to be an
exception) do not necessarily represent global minimum solution
(umm, this is not my field so I don't know the "correct term" to
use but the idea is that they are not in the lowest energetic
minimum state), just one of those local minima that are deep
enough for the fold to be "stable".
If so, then even if we solve all the math and computer problems
that exist, we still cannot tell which one of many possible
folds represents native protein. IMHO, the solution is again
in experiments, not in paper theory - we need to understand more
about just how and based on what proteins do fold in the cell.
- Dima
: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
:::