Mr YC Yap (eln118w at lindblat.cc.monash.edu.au) wrote:
: Hi there,
: I wonder if someone can help me with a problem.
: I'm writing a protein folding program that uses
: a simplified representation storing only the amino
: acid sequence, C-alpha coordinates and the Phi and
: Psi dihedral angles.
: At the end of the program, I need to reconstruct
: a detailed atomic model of the molecule. With the
: dihedral angles, I know the relative orientation
: of the backbone C, N and O atoms between one residue
: and its neighbour. But how do I get the starting
: coordinates of the FIRST N atom? Once I get that,
: I can work out the rest of the atoms.
(1) I think I may be misunderstanding your question, but
how about putting the first N atom at the origin (0,0,0) ?
If you mean the initial backbone N of each residue, that is
of course specified by the dihedral angles of the preceding
residue. Also, from your posting, don't forget to spec the
omega angle, unless that will always be 180 for your system.
(2) From my experience writing this same code, you will find
that you need to specify all bond lengths and bond angles
if you intend to create a structure which will be super-imposable
on a real structure. That is, if you try building a real
protein from its dihedral angles alone, you can do all the
code correctly and still have a result that is a *long* way
off in terms of RMS deviation. If you're trying to do
something that iteratively improves a model structure by some
other measure, like getting good pairwise distances (PMF),
and aren't worried about actually reproducing coords from a
crystal structure, this doesn't apply.
You *can* get 0.00 rmsd to a real structure by building from
scratch if you spec everything.
: Any ideas will be greatly appreciated.
: Thanks in advance.
: Alexander.
cheers,
rob.
--
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Rob Miller, Ph.D.
Biomolecular Structure and Modelling Unit (BSM),
Department of Biochemistry and Molecular Biology,
University College / Gower Street / London WC1E 6BT.
United Kingdom.
Tel: +44 171419 3896
Fax: +44 171380 7193
Internet: rmiller at bsm.bioc.ucl.ac.ukhttp://www.biochem.ucl.ac.uk/~rmiller
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