[MMTK] protein setup

michael.l.stoppelman.1 stoppeml@purdue.edu
Thu, 15 May 2003 11:26:09 -0500 (EST)


Hello all,

I wrote an inductive protein folder... It sometimes got between 6 to 12
angstroms on pretty short sequences like up to 20 - 30 residues. The
simulation gets really slow the after 30... I have the code if anyone
needs it.

Michael Stoppelman
mike@stoppelman.com


>
> Dear Asbjorn,
>
> As fantastic as MMTK is, I think even Konrad would admit defeat on the
> issue of protein folding ;)
>
> The closest you will get to generating a protein structure from the
> primary sequence is by some sort of homology modelling / threading (and
> even then the target and modelled sequences have to be virtually identical
> to get a sensible result!). You said "..WITHOUT reading an experimental
> PDB file (of the entire protein).." If you already have some of the
> structure and are modelling small gaps, this makes it slightly easier (but
> again, not exactly reliable). I think there is the functionality within
> MMTK to model small structure gaps - it's a matter of putting together the
> right routine. But to answer your question directly, translating a letter
> sequence to a sensible all-atom protein model with positions defined, is
> just not possible...at this moment in time.
>
> If you are still unsure, feel free to ask.
>
>
> Ben
>
> ----
> Ben Carrington
> Department of Pharmacology
> University of Cambridge, UK
>
>
> On Thu, 15 May 2003, Asbjorn Christensen wrote:
>
> > Dear MMTK users,
> >
> > 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)?
> >
> > Of course, this be done in a variety of not non-sense ways, e.g. a
> > "linear" chain. If anybody has a simple example of translating
> > a letter sequence to a sensible all-atom protein model (with positions defined),
> > this will be appriciated.
> >
> > PS:  is Examples/protein_construction.py in the online dokumentation
> >        up to date? Our MMTK installation has
> >        highest "last revision:" ==  2002-6-3
> >
> > Best wishes, Asbjorn
> > --
> > Asbjorn Christensen, PhD
> > CAMP, Physics Department, Building 307
> > Technical University of Denmark,
> > DK-2800 Lyngby, Denmark
> >
> > E-mail:       asbjorn@fysik.dtu.dk
> > Telephone: (+45) 45 25 32 27
> > Telefax:      (+45) 45 93 23 99
> > office:         room 257
> >
> >
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>
>
>
>
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