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

 Dr. Csaba Hetenyi wrote:
 
 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).
Sadly, I must say from personal experience I agree with you, but the problem remains that one often has to homology model a given receptor, because a xray/nmr structure is lacking. We as end-users of docking algorithms cannot wait for the experimental structures, because it is almost always the case that the crystal structure is one of the last pieces of information that is available (i.e. an experimental validation of a certain protein-ligand interaction has been published before the structures are known). Does this mean that computational docking is not useful in a practical sense? And what do you think about high-throughput homology modeling set-ups (ModBase,...)? 
 Regards
 Dominique
 
 Sorry, if i was too negative concerning HM.
 Best wishes,
 Csaba
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 Dominique Vlieghe, Ph.D.,
 Bioinformatics Core, Department for Molecular Biomedical Research (DMBR)
 VIB - Ghent University
 Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium
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