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Re: Many templates/targets



Thanks Karsten,

Your message was helpfull.  I think I'll try T-COFEE/SAP along with the 
ALIGN2D routine.  I've developed a few programs/scripts that helped me correct 
sequence ID codes to match atom files.  The TOP scripts also came in very 
handy in preparing these files.

Cvetan

Quoting Karsten Suhre <>:

> Hello Cvetan,
> 
>   from my own experience I know that Modeller is quite picky about correct 
> sequence (as it should). 
> 
> Anyhow, I would not use ClustalW alignments in the first place. When you
> model 
> a particular protein using several templates, you are *much* better off using
> 
> structural alignments instead of sequence based alignments alone. You could 
> use for example T-COFFEE together with SAP (or maybe Fugue, but I have no 
> experience with it). You would then use your PDB files from the start in the
> 
> alignment process, not unrelated Genbank sequences, and Modeller would thus 
> find all residues it needs in the alignment. Alternatively, there are 
> structrual alignments readily available at Homstrad for a large number of 
> proteins.
> 
> Note also that Modeller comes with a file modlib/CHAINS_all.seq. If you took
> 
> the sequences from this file in your ClustalW alignments it should work with
> 
> Modeller.
> 
> Hope this helps,
> 
> Kind regards,
> 
> Karsten.
> 
> > I'm trying to model 400+ proteins based on ~100 templates.  I have an
> > alignmentfile of 1500+ sequences comprising of the templates, targets and
> > others.  ClustalW was used to align the sequences.
> >
> > I have a few problems.
> > - The sequences in the alignment file do not match the aminoacids present
> > in the pdb files.  _Generally_ the pdb files contain more residues than
> > specified in the aligned sequence.  Therefore I have to either concatonate
> > the pdb files or specify the residues in the appropriate residues in the
> > alignment file. - The ID codes in the alignment file do not match the atom
> > file names. - There is no "second" line in each entry in the alignment
> > file.
> >
> > Although all this can be done manually, I can't help but wonder if there
> is
> > a way to automate/expidate the process.  A paper published by Sanhez and
> > Sali (1998) mentioned perl script that allowed for rapid progress through
> > the various steps involved with modelling.  Suggestions will be most
> > appreciated.
> >
> > Some of the pdb files are complexes.  If it can be avoided I'd prefer not
> > to use these structures .  However if I do decide to use some of them, I
> > plan to minimise the E via MD (cns) of the protein (minus the ligand)
> > before using it as a template.  What are people's thoughts about this?
> >
> > Many thanks
>