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Esperimento CASP

Cari colleghi,

stiamo organizzando la dodicesima edizione dell’esperimento CASP (www.predictioncenter.gov) che valuta la qualità’ di metodi di predizione di struttura di proteine e complessi di proteine. Vi
sarei veramente grata se voleste darci una mano sottomettendo
all’esperimento sequenze di proteine su cui state lavorando. Ci
servirebbero casi in cui la struttura non e’ ancora nota, ma ci si
aspetta ragionevolmente che lo sia entro la fine dell’estate o giu’
di li’. A quel punto se la struttura non fosse ancora pubblica, vi
chiederemmo di metterla a disposizione confidenzialmente ai
valutatori, non necessariamente ai predittori.

Ulteriori spiegazioni sono nel messaggio ufficiale che segue, ma
ovviamente potete contattarmi per altre informazioni.

Mi farebbe veramente piacere che anche la comunità italiana fosse visibile. Tra l’altro il meeting conclusivo dell’esperimento
quest’anno si terra’ in Italia, a Gaeta quindi potrebbe anche essere una buona occasione per vedere come passiamo il tempo noi computazionali!

Un grazie e . scusate il disturbo!

Anna Tramontano

Department of Physics
Sapienza University of Rome
P.le Aldo Moro, 5
00185 Rome
Tel: +39 06 49914550
e-mail: Anna.Tramontano@uniroma1.it
URL: http://www.biocomputing.it

As you may know, the CASP community experiments have been running once every two years since 1994, collecting information on soon to be solved structures from the experimental community, and passing on sequence data to the structure modeling community so that blind predictions of structure can be collected and assessed. Over that period CASP has seen enormous progress in the quality of modeled structures, but many problems remain, and further testing of prediction methods is imperative for advancing the field. CASP organizers collect target information for a three month season every two years, and in that period we can acquire around 100 targets, sufficient to evaluate the state of the art for most types of modeling.

In particular, we are interested in:

1. Novel folds and membrane protein targets. Last round we observed
some interesting methods developments for contact prediction and ab initio modeling, and it is important to be able to decisively
evaluate their effectiveness this CASP again.

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. Protein complexes and multimers.

The submission procedure is simple – there is a web page for
submitting targets, and a very experienced staff to deal with any
queries. We don’t need the structure in advance of its release by
the PDB, and if we are notified early enough (a minimum of three
weeks before release, more is better) there need be no delay in
structure release. We need all sorts of targets and in general
everything that has low coverage by the templates (<70% of the
sequence length) and relatively low sequence identity to the best
template (<50% ) will be appreciated. The time table is similar to previous CASPs: The prediction season
opens 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 and data-assisted 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.

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/casp12/targets_submission.cgi

After CASP prediction season is over we usually publish a paper on the experimentalists’ insights into the most interesting targets
(see below).

2015: Some of the most interesting CASP11 targets through the eyes of their authors. Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Proteins. 2015 Oct 16. doi: 10.1002/prot.24942. [Epub ahead of print]. PMID: 26473983.

2014: Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Proteins. 2014 Feb;82 Suppl 2:26-42.
doi: 10.1002/prot.24489. Erratum in: Proteins. 2015 Jun;83(6):1198. PMID: 24318984.

2011: Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure
prediction. Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T.
Proteins. 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21. PMID: 22020785.