On Sun, May 23, 2010 at 12:57 PM, David Briggs <[email protected]>wrote:
> I like to generate some models using the "Phyre" server > > ( http://www.sbg.bio.ic.ac.uk/~phyre/ ) > > Feed the best .pdbs into Mr Bump. > > Go and get coffee. Come back and find a solution with post-refmac > R/Rfree in the mid-30s. > > IMHO, Phyre models are often pretty good, and Phyre is worth running > on any sequence you are messing with - the output is nice and > informative. > My experience has been exactly the opposite; I've seen many people waste a lot of time this way. Phyre is a fold-recognition server - it is not intended to generate optimal, physically accurate models. It's possible that they've improved the output since I last used it, but I've seen plenty of models with overlapping sidechains and completely unrealistic packing. Use Modeller or Rosetta (both also available as web servers) if you want as accurate a homology model as possible. Even so, if you can find homologs in the PDB with better than 30% sequence identity, you'll probably have at least as much success using those as search models, after judicious pruning (which I think MrBUMP can do automatically). This is not to say that homology modelling isn't occasionally useful for MR, but it is not the first thing I'd try unless I had put a great deal of thought into the pipeline and had a large cluster to run it on. I know the JCSG has had some luck with this approach, but they have full-time programmers and something like 400 CPUs. -Nat
