[MMTK] Re: mmtk digest, Vol 1 #200 - 3 msgs

Ivan Rossi ivan@biocomp.unibo.it
Mon, 19 May 2003 10:47:05 +0200 (CEST)


> > is there any simple way to initialize the position of atoms > in a
> protein directly from a given letter sequence ["Ala", "Gly", "Tyr" >
> ...] WITHOUT reading an experimental PDB file (of the entire protein)?
> 
> No, not at this time. Of course, MMTK cannot solve the protein
> folding problem, so the choice for such an operation would be
> limited to generating standard patterns such as alpha helices and
> beta sheets. I am not sure there is really any use for that.

There is use for it. It is actually a very convenient way to initialize
conformation in any folding orloop modelling/reconstruction experiment that
you want to do. Or if you want to develop modelling codes that are not just
MD-related.

We tried to prototype a folding code on top of MMTK and the first thing we
had to do was to write a kludge to generate an extended conformation from a
protein sequence. If it will ever leave the kludge state i may send it back
to konrad to be considered for inclusion in MMTK.  However if someone will
submit earlier a consistent general-purpose conformer generator for
sequences, i will be happy to throw away mine.

--
Ivan Rossi, Ph.D. - BioDec & CIRB Biocomputing Unit
e-mail: ivan@biocomp.unibo.it,  i.rossi@computer.org 
Web: http://www.biocomp.unibo.it/ivan
Shameless Self-Promotion: www.biodec.com