energy of half protein

[__k]

Hello
I think it's not directly related
but i have a question if you can answer it for me :)
i wanna know if there's a way to know crease energy before the final structure is made..
that is, can we know in the middle of a structure, if it's rmsd 0 ?
also, i would like to know how the minimization / trajectory-projection
works..
does it take the best ones, and then makes variations upon it?
how does it know which is the best part of the protein to base the variations upon?

hmm, if it's possible to know from advance
the best energy in the middle of building it
i guess we wouldn't be here..
so, i'm still kinda baffled how it manages to know which ones to generate.
since it's obviously different than gen0 random sequences.

thank in advance for anyone answering my question.
:thumbs: :scared: :moon: :cool:

[Brian the Fist]

Originally posted by __k
Hello
I think it's not directly related
but i have a question if you can answer it for me :)
i wanna know if there's a way to know crease energy before the final structure is made..
that is, can we know in the middle of a structure, if it's rmsd 0 ?
also, i would like to know how the minimization / trajectory-projection
works..
does it take the best ones, and then makes variations upon it?
how does it know which is the best part of the protein to base the variations upon?

hmm, if it's possible to know from advance
the best energy in the middle of building it
i guess we wouldn't be here..
so, i'm still kinda baffled how it manages to know which ones to generate.
since it's obviously different than gen0 random sequences.

thank in advance for anyone answering my question.
:thumbs: :scared: :moon: :cool:

The energy of a protein requires the entire protein to compute. Looking at just part of it won't necessarily give you an accurate picture since a piece of the protein you havent built yet may contribute beneficially to the total energy.

It takes the lowest RMSD (or lowest energy) whole structure from gen. 0 and then 'minimizes' the energy mostly to get rid of any overlapping atoms, and tidy up the geometry a bit.

The next generation of structure will all be generated by slightly 'wiggling' that seed structure in random directions