Hi Susy,
Before going into details: you have to get the alignment right. After
that, you may look into packing quality and geometry of your models.
Regarding the parameters you are interested in: I talked to a guy from
the Sali lab (Modeller) about quality assessment of homology models. He
recommends to compare the gromos or anolea profiles per residue (or
whatever packing score your software uses) to the template. In case
there is gap: pay attention to the alignment! Regarding cut-off values
(what's ok and what not) you may want to look into published work on
your modeling software and/or contact the authors directly.
Another way to look at model quality, and maybe more significant, is to
check geometry (clashes, rotamers, bond angles etc.). You could use
MolProbity for that. The supplementary material of the following article
contains a good example (Table S1) on the evaluation of a trimer interface:
http://www.ncbi.nlm.nih.gov/pubmed/20457942
Good luck!
Oliv
On 02/07/11 01:13, Susy Rao wrote:
Dear Community,
I have a question regarding protein model quality for introduction of
point mutations which should increase solibity/stability of my protein
of interest.
I plan to do homology models so that I can check the most promising
amino acids.
Which quality/resolution of the model do I need?
Which parameters would you check (gromos, anolea), and what would you
use as cut-off values?
At the moment I thought, that it could be interesting to model a
homologue of my protein and check the RMSDs with the crystal structure.
Maybe you know some good literature, describing this?
Thank you
Susy
--
Oliv Eidam, Ph.D.
Postdoctoral fellow
University of California, San Francisco
Dept. of Pharmaceutical Chemistry
1700 4th Street, Byers Hall North, Room 501
San Francisco, CA 94158 - Box 2550
Phone: 415-514-4253
Fax : 415-514-4260
Email: [email protected]
