CASP (Critical Assessment of protein Structure Prediction) is in search
for targets for the upcoming CASP14 modeling experiment (starting next
Monday, May 18, 2020).
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 in the unofficial 'Olympics in the protein
structure modeling', as CASP is often dubbed. Results of CASP
experiments are assessed by prominent specialists in the field
(http://predictioncenter.org/index.cgi?page=assessors_list
<http://predictioncenter.org/index.cgi?page=assessors_list>), and
published in special issues of the journal PROTEINS (see
https://onlinelibrary.wiley.com/doi/10.1002/prot.25823
<https://onlinelibrary.wiley.com/doi/10.1002/prot.25823> for the latest
issue).
The success of CASP depends on the generosity of the structure
determination community, and over the years more than 150 structure
determination groups provided targets for the challenge. We need
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 have also extended CASP to include
modeling assisted by sparse experimental data, in collaboration with
experimental groups in NMR, SAXS, and crosslinking. For that, protein
material is needed (of course this is not expected for most targets, but
if available, it would be much appreciated!).
If you have anything suitable, we would appreciate if you get in touch
with us by writing to c...@predictioncenter.org or suggest your protein
directly through the CASP14 target entry page:
http://www.predictioncenter.org/casp14/targets_submission.cgi. If your
structure is ready for the PDB deposition, we encourage you to mark it
as a "CASP target" in the PDB's submission system. 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 through the website provided above.
CASP target providers are regularly invited to contribute to special
issue papers, for example:
2019: Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ,
Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M,
Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD,
Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV,
Michalska K, Mir-Sanchis I, Mitra A, Moult J, Phillips GN Jr, Pinkas DM,
Rice PA, Tong Y, Topf M, Walton JD, Schwede T. (2019). Target highlights
in CASP13: experimental target structures through the eyes of their
authors. Proteins 87 (12), 1037-1057. Published online: 2019 Aug 23.
doi: 10.1002/prot.25805. PMID: 31442339
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
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:
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
Hoping for your help in obtaining wide range of targets for CASP14.
Thanks,
CASP organizing committee:
John Moult, President, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, University of Basel, Switzerland
Maya Topf, UCL, UK
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