In article <4ndovp$380 at manuel.anu.edu.au>, Shoba.Ranganathan at anu.edu.au (Shoba.Ranganathan) writes:
|>|> I'm looking for references that state the minimum sequence identity
|> required for homology modelling, and the percentage in the reference
|> (in case I can't find the article).
I assume you mean for SUCCESSFUL homology modeling? You can model anything you
want; whether it is useful or meaningful is another question.
I could point out a couple attempts that failed (in my view) with 18-20%
identity. Some of the reasons for the failure: 1) despite the overall
identity numbers, there was no homology at all for one of the regions modelled.
1b) This fact was obscured by incorrect sequence alignments.
2) The modelling attempts may have been influenced by an incomplete and
incorrect crystal structure of a third homologous protein.
Banci, Carloni & Savellini (1994) Biochemistry 33, 12356-12366.
Smith, Du & Loew (1995) Nuclear Magnetic Resonanc of Paramagnetic
Macromolecules, Kluwer Academic publishers, the Netherlands, pp. 75-93.
naturally, the authors would probably prefer to dwell on the positive aspects,
such as correct placement of some or all of the active site residues, and not
on the fact that some residues were mis-placed by tens of Angstroms.
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That's MISTER Peanut to you!
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Dave Schuller
University of California-Irvine
schuller at uci.edu
modern man in a post-modern world
