Bioinformatics Vol. 19 no. 8 2003
Pages 1015-1018
© 2003 Oxford University Press
3D-Jury: a simple approach to improve protein structure predictions
1 BioInfoBank Institute, Limanowskiego 24A,
60-744 Poznan, Poland
2 Stockholm Bioinformatics Center,
AlbaNova, Stockholm University, 10691 Stockholm, Sweden
3 Bioinformatics, Department of Computer
Science, Ben Gurion University, 84015 Beer-Sheva, Israel
Received on November 7, 2002
; revised on January 9, 2003
; accepted on January 14, 2003
Motivation: Consensus structure prediction methods (meta-predictors) have higher accuracy than individual structure prediction algorithms (their components). The goal for the development of the 3D-Jury system is to create a simple but powerful procedure for generating meta-predictions using variable sets of models obtained from diverse sources. The resulting protocol should help to improve the quality of structural annotations of novel proteins.
Results: The 3D-Jury system generates meta-predictions from sets of models created using variable methods. It is not necessary to know prior characteristics of the methods. The system is able to utilize immediately new components (additional prediction providers). The accuracy of the system is comparable with other well-tuned prediction servers. The algorithm resembles methods of selecting models generated using ab initio folding simulations. It is simple and offers a portable solution to improve the accuracy of other protein structure prediction protocols.
Availability: The 3D-Jury system is available via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/) to the academic community.
Contact: leszek{at}bioinfo.pl
Supplementary information: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/)
* To whom correspondence should be addressed.
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B. Bottcher, S. Unseld, H. Ceulemans, R. B. Russell, and H. Jeske Geminate Structures of African Cassava Mosaic Virus J. Virol., July 1, 2004; 78(13): 6758 - 6765. [Abstract] [Full Text] [PDF]
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D. E. Kim, D. Chivian, and D. Baker Protein structure prediction and analysis using the Robetta server Nucleic Acids Res., July 1, 2004; 32(suppl_2): W526 - W531. [Abstract] [Full Text] [PDF]
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K. Ginalski, M. von Grotthuss, N. V. Grishin, and L. Rychlewski Detecting distant homology with Meta-BASIC Nucleic Acids Res., July 1, 2004; 32(suppl_2): W576 - W581. [Abstract] [Full Text] [PDF]
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J. Towpik, A. Chacinska, M. Ciesla, K. Ginalski, and M. Boguta Mutations in the Yeast MRF1 Gene Encoding Mitochondrial Release Factor Inhibit Translation on Mitochondrial Ribosomes J. Biol. Chem., April 2, 2004; 279(14): 14096 - 14103. [Abstract] [Full Text] [PDF]
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M. DLAKIC and D. TOLLERVEY The Noc proteins involved in ribosome synthesis and export contain divergent HEAT repeats RNA, March 1, 2004; 10(3): 351 - 354. [Abstract] [Full Text] [PDF]
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K. Ginalski, L. Rychlewski, D. Baker, and N. V. Grishin Protein structure prediction for the male-specific region of the human Y chromosome PNAS, February 24, 2004; 101(8): 2305 - 2310. [Abstract] [Full Text] [PDF]
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