Hello everybody,
my question has already been posted a couple of times - however these posts date back a couple of years. That is why I hope to find new answers to this topic.
Modeller (9v7) does not recognize phosphotyrosine residues (Phosporylated tyrosines, PTR). There are three options to deal with such undefined residues:
1. Use Tyrosine instead (and optionally after modelling: replace with phosphotyrosine und minimize) This might be a good choice, if the residues were in areas far away from the region under investigation
2. Use Block Residue (rigid body) - not the most accurate way, but a good workaround (http://salilab.org/modeller/9v7/manual/node95.html)
3. Define the unknown residue according to the manual/FAQ (http://salilab.org/modeller/FAQ.html#8)
I would prefer the third option and define them myself, but as the manual states, this is a "painful" process. I wonder if anyone has generated the needed files/entries for the modeler libraries. There is a page in the Modeller Wiki that allows upload of these customized files. It is empty however. Since I currently do not have access to QUANTA or CHARMM, I cannot generate the files myself. I also wonder why the library file for residues in modeller 9v7 still dates back to 1993?
I hope someone can help. Thank you in advance,
Cheers
Jan H. Loehr University of Hamburg, Germany
On 02/24/2010 03:23 AM, Jan H. Löhr wrote: > my question has already been posted a couple of times - however these posts > date back a couple of years. That is why I hope to find new answers to this > topic.
The three options you quote are still the same...
> I would prefer the third option and define them myself, but as the manual > states, this is a "painful" process.
Note also that Modeller generates restraints based on homology, and its database contains many examples of TYR aligned with other standard template residues, but none of phosphotyrosine, so you will get fewer restraints on these residues.
> I wonder if anyone has generated the needed files/entries for the modeler > libraries. There is a page in the Modeller Wiki that allows upload of these > customized files. It is empty however. > Since I currently do not have access to QUANTA or CHARMM, I cannot generate > the files myself.
The parameter and topology files are, however, just text files and you can create them in any text editor. You may be able to find suitable files at www.charmm.org; Modeller parameter/topology files are basically the same as CHARMM files, just with some atom names modified to match PDB naming.
> I also wonder why the library file for residues in modeller 9v7 still dates > back to 1993?
The topology of the 20 standard amino acids hasn't changed since 1993...
Ben Webb, Modeller Caretaker
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Jan H. Löhr -
Modeller Caretaker