The low RMSD between model and template is expected when you are using a
single template, even at low sequence identity, the model does not have much
of a choice but to follow the template. How low is the target-template
sequence identity in this case?. The many bad contacts may be a consequence
of misalignments rather than large structural differences between target and
template. If the sequence identity is sufficiently low (<30%) alignment
errors become more and more of an influence on the accuracy of the model.
You may want to try some alternative alignments (maybe some profile-based
alignment) and see if the bad contacts dissappear.
I hope this helps.
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
> -----Original Message-----
> On">mailto:]On Behalf Of Margot
> Sent: Thursday, December 05, 2002 4:57 AM
> Subject: low sequence identity
> Dear Modeller support,
> I am modeling at low sequence identity and I believe to have the
> problem: The homologous scaffold (comprising a core of beta
> strands) of my
> target, after a fisrt round of modeling, displays a
> (suspiciously) low RMSD
> with respect to the template, and a LOT of bad contacts involving the
> hydrophobic core. Consequently I think that in my target
> secondary structure
> motifs should be arranged more spaciously. How can I accomplish
> this in terms
> of additional modeling restraints, or chopping up the alignment
> and modeling
> in pieces, or whatever will work?