mAb INITIO PREDICTION

I need a function that can distinguish from native and non native conformation, so correct or non
correct. Usually the most high score minimizes the energy level, and it’s difficult because the
number of atoms to put in space is huge, think about a protein of 100 aa, every aa is made up of 20
atoms. Each atom has 3 values, x, y, z, and can be every possible value in that distance allowed.
The range of solution is very high, for every atom I have to chose a solution, if I want to test a given
number of solution is a thing, but considering every possibl solution starting from zero is very
difficult: starting from an aa, then I have to consider every its possible position for each atom, that
has 3 coordinates; then I have to test each of that possibilities with the same calculation for each aa.
Aa are bound each other through peptide bond. Only the 1st one has a free NH2 group (or COOH).
The other are engaged in peptide bonds. This bond is important because among a peptide bond, all 6
atoms implied in this are all located in a plane, are forced to be there and this makes that those
atoms are not really free to be located everywhere, each peptide bond constrains 6 atoms to be on a
certain plane. This simplifies with the fact that a bond in a protein is defined by 2 numbers, the two
angle made by alfa-carbon (which carries R-group) binding with NH- and CO- of adjacent amino
acid. So, I can DEFINE THE WHOLE BACKBONE OF A PROTEIN made u of 100 aa with 2
numbers for each bond, something like 200 numbers. Much less than starting point!
Now the problem is shifted to how small is the minimum rotation value considered: 1°, 0.1° or
0.01°? 360, 3600 or 36000 possibilities?
Things are simpler than this. The real world has much constrains, so the two angles can’t be
together zero, because that would put atoms really close. I won’t test 0 and 0, but either 0 and 0.1
and sooo on. The impossible combination are much more than possible combination.
Real proteins are much simpler, if I query a database of 1000 of peptide bonds I will see that the
majority of angles assumed by psi and fi will be distributed in a really small area on the square (that
is a plot of the most possible combination of angles without considering the impossible). The most
frequent possibilities will concentrate in those areas of alfa helix or beta sheets structures:
essentially all proteins start by folding in these 2 structures.
Why helix i so common? Are not easy things to think  has less energy
Beta sheet also common. Different sequences, in sense that ok could be the same peptide, but
distant  not adjacent amino acids. Parallel or antiparallel.
Note that in helix I’ve not considered the side chains and how they can organize.Helix adjust in a
way that can be useful for protein structure. ex I see in a sequences all hydrophobic are in a side and
hydrophilic are in the other side of the protein. The residues of a protein organizes in such wway
functional, maybe that part of the protein is a hydrophobic domain. A globular protein will organize
in such way the hydrophobic aa will be at the center and the hydrophilic will be exposed, so I
already know that is reasonable to expect the peptide interacting with an antibody is made up
basically of hydrophilic amino acids.
Note that, the proteins reach the last state step by step. Each structure has to change each into the
other ti reach the most stable, so I add more things to consider and the things will complicate: but
this is nothing problem if compared to the earlier problem.
If I use sink which means already existing models, the things are simpler.
Alfa helix, beta sheet, coil and turn.