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Subject: models for MR

>From Katherine Kantardjieff:

We have tried this with some success on several TB proteins as part of =
the efforts of the TB Structural Genomics Consortium. These have not yet =
been formally published. Basically, we have produced both homology and =
comparative models using SwissModeller or Modeller, as well as other =
servers such as 3D PSSM and the prediction servers at LLNL. Each model =
is slightly different, but can be evaluated using whatCheck, ProCheck, =
ProsaII etc. We have also used different MR algorithms, and epmr and =
amore seem to work the best, although one may find a solution while the =
other won't. My advice is to try each model and each MR algorithm =

We then take the MR results and run the initial maps through phase bias =
removal shake& warp (Segelke and Rupp)before viewing. In the best case, =
we had an interpretable map and model that could be rebuilt in a day =
with XtalView. In the worst case, we obtained a map with interpretable =
features, but still poor connectivity and a great deal of work ahead. In =
this case, the hybrid fold and sequence match was low to anything in the =
available databases. But, we may still be able to pull it out.

Professor Katherine Kantardjieff
Director, W.M. Keck Foundation Center for Molecular Structure
Department of Chemistry and Biochemistry
California State University Fullerton
800 N. State College Blvd.
Fullerton, CA 92834-6866
Office: (714) 278-3752
eFax: (734) 939-4225
eMail:  <">mailto:>