Home
  >  
Section 12
  >  
Chapter 11,464

The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2

Fischer, D.; Elofsson, A.; Rychlewski, L.

Protein Engineering 13(10): 667-670

2000

ISSN/ISBN: 0269-2139
PMID: 11112504
DOI: 10.1093/protein/13.10.667
Accession: 011463859
Download citation:  
Text
  |  
BibTeX
  |  
RIS
In this commentary, we describe two new protein structure prediction experiments being run in parallel with the CASP experiment, which together may be regarded as the 2000 Olympic Games of structure prediction. The first new experiment is CAFASP, the Critical Assessment of Fully Automated Structure Prediction. In CAFASP, the participants are fully automated programs or Internet servers, and here the automated results of the programs are evaluated, without any human intervention. The second new experiment, named LiveBench, follows the CAFASP ideology in that it is aimed towards the evaluation of automatic servers only, while it runs on a large set of prediction targets and in a continuous fashion. Researchers will be watching the 2000 protein structure prediction Olympic Games, to be held in December, in order to learn about the advances in the classical 'human-plus-machine' CASP category, the fully automated CAFASP category, and the comparison between the two.

PDF emailed within 0-6 h: $19.90




Related References

Fischer, D.; Barret, C.; Bryson, K.; Elofsson, A.; Godzik, A.; Jones, D.; Karplus, K.J.; Kelley, L.A.; MacCallum, R.M.; Pawowski, K.; Rost, B.; Rychlewski, L.; Sternberg, M. 1999: CAFASP-1: Critical assessment of fully automated structure prediction methods Proteins Suppl 3: 209-217
Fischer, D.; Rychlewski, L. 2003: The 2002 Olympic Games of protein structure prediction Protein Engineering 16(3): 157-160
Kryshtafovych, A.; Moult, J.; Bales, P.; Bazan, J.Fernando.; Biasini, M.; Burgin, A.; Chen, C.; Cochran, F.V.; Craig, T.K.; Das, R.; Fass, D.; Garcia-Doval, C.; Herzberg, O.; Lorimer, D.; Luecke, H.; Ma, X.; Nelson, D.C.; van Raaij, M.J.; 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 Suppl. 2: 26-42
Zhang, Y. 2009: I-TASSER: fully automated protein structure prediction in CASP8 Proteins 77(Suppl 9): 100-113
Bystroff, C.; Shao, Y. 2002: Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA Bioinformatics 18(Suppl 1): S54-S61
Lei, C.; Tamim, S.; Bishop, A.J.; Ruan, J. 2013: Fully automated protein complex prediction based on topological similarity and community structure Proteome Science 11(Suppl 1): S9
Brocklehurst, S.M.; Perham, R.N. 1993: Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure Protein Science: a Publication of the Protein Society 2(4): 626-639
Koehl, P.; Levitt, M. 1999: A brighter future for protein structure prediction (Third Community Wide Experimental on the Critical Assessment of Techniques for Protein Structure Prediction) (California, USA, December 13017, 1998) Nature Structural Biology 6(2): 108-111
Senior, A.W.; Evans, R.; Jumper, J.; Kirkpatrick, J.; Sifre, L.; Green, T.; Qin, C.; Žídek, A.; Nelson, A.W.R.; Bridgland, A.; Penedones, H.; Petersen, S.; Simonyan, K.; Crossan, S.; Kohli, P.; Jones, D.T.; Silver, D.; Kavukcuoglu, K.; Hassabis, D. 2019: Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13) Proteins 87(12): 1141-1148
MacCarthy, E.; Perry, D.; Kc, D.B. 2019: Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction Methods in Molecular Biology 1958: 15-45
Osipovitch, M.; Lambrecht, M.; Baker, C.; Madha, S.; Mills, J.L.; Craig, P.A.; Bernstein, H.J. 2015: Automated protein motif generation in the structure-based protein function prediction tool ProMOL Journal of Structural and Functional Genomics 16(3-4): 101-111
Lobanov, M.I.; Bogatyreva, N.S.; Ivankov, D.N.; Finkel'shteĭn, A.V. 2009: Protein structure prediction from analogy. I. new database of spatially similar and dissimilar structures of protein domains for testing and optimization of prediction methods Molekuliarnaia Biologiia 43(4): 722-732
Tran, N.H.; Xu, J.; Li, M. 2022: A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction Briefings in Bioinformatics 23(1)
Yu, M.. Lobanov; Bogatyreva, N.S.; Ivankov, D.N.; Finkel, A.V.'shtein 2009: Analogy-based protein structure prediction: I. A new database of spatially similar and dissimilar structures of protein domains for testing and optimizing prediction methods Molecular Biology 43(4): 665-676
Kouza, M.; Faraggi, E.; Kolinski, A.; Kloczkowski, A. 2017: The GOR Method of Protein Secondary Structure Prediction and its Application as a Protein Aggregation Prediction Tool Methods in Molecular Biology 1484: 7-24
Aloy, P.; Querol, E.; Aviles, F.X.; Sternberg, M.J. 2001: Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking Journal of Molecular Biology 311(2): 395-408
Yan, C.; Xu, X.; Zou, X. 2016: Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction Structure 24(10): 1842-1853
Siew, N.; Elofsson, A.; Rychlewski, L.; Fischer, D. 2000: MaxSub: an automated measure for the assessment of protein structure prediction quality Gcb'99 German Conference on Bioinformatics (Hanover 1999) 16(9): 776-785
Siew, N.; Elofsson, A.; Rychlewski, L.; Fischer, D. 2000: MaxSub: an automated measure for the assessment of protein structure prediction quality Bioinformatics 16(9): 776-785
Roy, A.; Kucukural, A.; Zhang, Y. 2010: I-TASSER: a unified platform for automated protein structure and function prediction Nature Protocols 5(4): 725-738