Re: CCL:predict 3D structure from sequence (fwd)
- From: "Felipe Pineda, PhD"
- Subject: Re: CCL:predict 3D structure from sequence (fwd)
- Date: Mon, 06 Sep 2004 12:35:58 +0200
Dear Csaba and all,
"Dr. Csaba Hetenyi" wrote:
> > The first one called Camparative Protein Modeling, which requires a 3d
> > structure of a protein, which has >30% sequence Similarity
> > target. It's pretty reliable. The second approach has lower success
> > rate..
> I'd rather not say "it is pretty reliable". In my view, sequence
> similarity (30 % or above) is not a sufficient only a necessary
> requirement of possible homology modeling (HM).
> A "nice" example of failure of HM was recently mentioned in
> al. Science 305 (2004) 683-686. E.g. CYPs are "excellent"
> proteins not appropriate for HM.
According to your own necessary/sufficient conditions this wouldn't be a
example, since the authors state that templates available for
of CYP3A4 display just sequence identities < 30% with the target. On p.
"The most widely used templates for modeling CYP3A4 are the P450
Bacillus megaterium (P450 BM3) and Saccharopolyspora erythraea (P450
of which share less than 25% sequence identity with CYP3A4."
Without the intension of self-advertising, I can refer you to our
Pineda, L.F. and Hilgenfeld, R.) recent paper published on DDT
the utility of homology models in the drug discovery process, wich
contains a, in
our opinion, balanced discussion on the performance of the comparative
method in different applications.