[phenixbb] Protein structures sought for CASP13

Paul Adams pdadams at lbl.gov
Fri Apr 20 06:35:57 PDT 2018

Posted on behalf of the CASP organizing Committee:

Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. About 100 modeling groups from around the world participate. Results of CASP experiments are published in special issues of the journal PROTEINS (e.g., CASP12: https://onlinelibrary.wiley.com/toc/10970134/86/S1).

The success of CASP depends on the generosity of the structure determination community. We are now requesting targets for CASP13 experiment, which will launch at the beginning of May. The CASP community needs modeling targets over a wide range of difficulty, for modeling with and without the aid of templates. X-ray, NMR and cryo-EM structures are welcome. We are particularly interested in membrane proteins, protein complexes, and cryo-EM structures. We are also extending CASP to include more modeling assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, SANS, crosslinking, and FRET. For that, protein material is needed (of course this is not expected for most targets, but if available, it would be much appreciated!).

So, if you have anything suitable, we encourage you to mark your PDB deposition as a "CASP target" in the PDB's submission system. Alternatively, you can suggest your protein to CASP directly through the CASP13 target entry page: http://www.predictioncenter.org/casp13/targets_submission.cgi.

For those of you who have not provided targets to CASP before, the procedure is simple and fast. 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. More details are available on the web site.

CASP target providers are regularly invited to contribute to special issue papers, for example:

2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 28960539

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. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 26473983 

2014: 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. (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. Proteins 82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 24318984

2011: 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.  (2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 (S10), 6-20. doi: 10.1002/prot.23196. PMID: 22020785


CASP organizing committee:

John Moult, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, University of Basel, Switzerland

Get in touch: casp at predictioncenter.org
More information: http://www.predictioncenter.org/casp13/index.cgi
Submit a target: http://www.predictioncenter.org/casp13/targets_submission.cgi

Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]

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