> Phyre is a fold-recognition server...
And one might argue that "recognising the fold", getting the
loops/boundaries in the right place is the first step towards getting
MR to work properly - which is what I think Phyre does rather well.
But I absolutely agree that an approach like this requires that you
actually look at the Phyre models, and make sure that they are vaguely
sensible.
And yes, I would always run Mr Bump with most of the various model
modification bells-and-whistles activated, to get poly-ala, chainsawed
models etc.
But hey - this is just another anecdote, and "the plural of anecdote
is not data" :-)
Cheers,
Dave
============================
David C. Briggs PhD
Father, Structural Biologist and Sceptic
============================
University of Manchester E-mail:
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============================
http://xtaldave.wordpress.com/ (sensible)
http://xtaldave.posterous.com/ (less sensible)
Twitter: @xtaldave
Skype: DocDCB
============================
On 23 May 2010 21:27, Nathaniel Echols <[log in to unmask]> wrote:
> On Sun, May 23, 2010 at 12:57 PM, David Briggs <[log in to unmask]>
> 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
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