[Molvis-list] protein visualisation

[Kevin Karplus]

There are sites that attempt to do prediction even for new folds.
The models are not good, though, unless there is a homolog in PDB.

There were 98 servers registered for CASP7, 56 of which were producing
3D models, 7 of which were producing alignments.  The other 35 were
either entered in subcategories (doman prediction, contact prediction,
...) or were non-functional.

I don't know how many of the 56 servers are actually free to the
public with reasonable wait times.  (One of the best at casp6 was
Robetta, and there is a free Robetta server, but the queue is months long.)
The one that currently looks best in CASP7 is the Zhang-Server, but I
think that requires even more processors than Robetta and is not
publically available (I may be wrong on that, as the Zhang-Server is a
new entry to CASP.)

I have a new server that is decent (better than my old servers and
easier to use), but not top of the line any more.  It does about as
well as human-assisted prediction 2-4 years ago, but there are
meta-servers doing somewhat better.  Our server only uses one (rather
ancient) CPU per job, so responses take 10-24 hours.  This means that
we can offer the service for free:

http://www.soe.ucsc.edu/research/compbio/SAM_T06/T06-query.html

In addition to the model, there are lot of other useful files
provided: sequence logos, predictions of local structure, ...  .

------------------------------------------------------------
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors & Chair of Education Committee, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Affiliations for identification only.