[phenixbb] Call for not-yet-released structures as candidates for protein structure predictors

Susan Tsutakawa setsutakawa at lbl.gov
Tue Apr 17 15:53:17 PDT 2018

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: Proteins Vol 86, Issue S1, March 2018).

The thirteenth CASP round is scheduled to start on May 1, 2018. The
organizing committee is particularly keen to include many cryo-EM-derived
structure targets in this round.

The success of CASP depends on the generosity of the structure
determination community. Modeling targets are needed over a wide range of
difficulty, for modeling both with and without the aid of templates.
Targets that can be modeled based on structural templates should ideally
have 50% or less sequence identity to the templates. Access to the
structure in advance of its release by the PDB or its publication is not
needed. With sufficient notification to CASP (a minimum of three weeks
before release, more is better) there is no need to delay structure
release. If you have recently determined a novel protein structure and will
be depositing it to PDB, please suggest it as a target for CASP by visiting
www.predictioncenter.org/casp13/targets_submission.cgi. If you have any
questions please contact [log in to unmask]

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: 2896053
    2016: 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:
    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: 2431898
    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: 2202078

Posted on behalf of the 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
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