Dear colleagues,
This is a follow up to our earlier message, requesting prediction
targets for CASP10.
First THANK YOU to those who came forward with targets -- really much
appreciated, and has helped get this CASP off to a great start. We now
have over 70 targets released.
Second, please send more targets! There is still a month of the
prediction season to run, and the first batch of targets is all used up.
The details of what is needed and so on are below -- just like in the
earlier message.
Again, thanks to the structural biology community for all your help, in
this and previous CASPs (1):
/CASP10 organizers: Torsten Schwede, Andriy Kryshtafovych, Anna
Tramontano, Krzysztof Fidelis and John Moult./
*The specifics:*
We need all sorts of targets but in particular:
1. (More than ever) novel folds and membrane protein targets -- even
with the extended collection season provided by CASP ROLL
(http://predictioncenter.org/casprol/index.cgi) there will be still a
shortage. This round there are some interesting methods developments for
ab initio modeling, and it is important to be able to decisively
evaluate their effectiveness.
2. A diversity of comparative modeling targets. Cases where the there is
fairly high sequence identity (30-50%) between the target structure and
an available template are valuable for testing the degree to which model
accuracy can approach that of experiment, particularly in functionally
critical regions. Cases with lower sequence identity to template, right
down to undetectable, are valuable for testing the ability of the
methods to detect remote homologs, to overcome challenging alignment
difficulties, to make use of multiple templates, and to build regions of
the structure not obviously available from a template.
3. Targets containing significant amounts of disordered structure, so as
to test the ability of methods to identify these regions. Disorder
identified by absence of density in crystallography is current the main
source and very useful, but its important to have cases where the nature
of the disorder has been established by other means, such as NMR.
4. Some targets will also be used to test methods of structure
refinement. In these cases, the best model received for a target will be
released to the refinement community, who will subsequently submit new
models. This too is an area where there have been some exciting
developments in the last year, so we are hoping for significant
progress. Refinement targets are selected based on the nature of the
errors in the initial models. Because of the extended process, these
targets need to be available for longer before release of the
experimental structure.
The time table is similar to other CASPs: The prediction season opened
at the beginning of May, and will run until the end of July. We are
releasing targets continuously throughout that period, as evenly spaced
as possible, aiming for about 100 targets altogether. Each target will
be available for prediction for a period of three weeks, although in
some cases we request a longer period to allow it to be used to test
refinement methods. It is of course important that there not be any kind
of public release of the experimental structure (including things like
pictures on web pages or abstracts) until after the predictions for that
target are closed.
As many of you know, it's fairly simple, with just two things to bear in
mind. First, because of the timing framework, there needs to be at least
a month between the submission date and any release of the structure.
Second, we ideally need the experimental co-ordinates by the beginning
of August and definitely by the end of August, so that the predictions
can be assessed. At that point, they can be kept confidential if
necessary, though we would like to provide them to predictors of your
structure at the beginning of November at the latest, so that can see
how well they have done. Participants would also usually like to be able
to show slides and discuss their predictions at the meeting at the
beginning of December.
So, if you have any thing suitable, we would be most grateful if you
would go to the target entry page:
http://www.predictioncenter.org/casp10/targets_submission.cgi
1. 'Target highlights in CASP9: Experimental target structures for the
critical assessment of techniques for protein structure prediction.'
Kryshtafovych A et al. PROTEINS 2011;79 Suppl 10:6-20. doi:
10.1002/prot.23196. Epub 2011 Oct 21.
