Subject: Re: CCL:predict 3D structure from sequence (fwd)

From: "Dr. Csaba Hetenyi" <csaba(at)ovrisc.mdche.u-szeged.hu>
Date: Fri, 3 Sep 2004 11:52:35 +0200 (CEST)

> The first one called Camparative Protein Modeling, which requires a 3d
> structure of a protein, which has >30% sequence Similarity comparing to
> 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 Williams et
al. Science 305 (2004) 683-686. E.g. CYPs are "excellent" examples of
proteins not appropriate for HM. 
Extensive, uncontrolled use of HM (or - horribile dictu - HM and
consecutive docking on a HMed target contributes to rising (and - in this
case - right) scepticism of experimental guys against modeling (against
us).
Sorry, if i was too negative concerning HM.
Best wishes,
Csaba