Consensus fold recognition by predicted model quality

Series on Advances in Bioinformatics and Computational Biology

Volumn 1, Issue , 2005, Pages 73-83

  Xu, Jinbo ^a   Yu, Libo ^a   Li, Ming ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; PROTEINS; SUPPORT VECTOR MACHINES;

CONSENSUS METHODS; CRITICAL ASSESSMENT; FUNCTIONAL ANNOTATION; PROTEIN FOLD RECOGNITION; PROTEIN STRUCTURE PREDICTION; STRUCTURAL MODELING; STRUCTURE PREDICTION; SUPPORT VECTOR MACHINES REGRESSION;

FORECASTING;

EID: 84863012869     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1142/9781860947322_0008     Document Type: Conference Paper

References (26)

1. J. Moult, T. Hubbard, F. Fidelis, and J. Pedersen. Critical assessment of methods on protein structure prediction (CASP)-round III. Proteins: Structure, Function and Genetics, 37(S3):2-6, December 1999.
2. J. Moult, F. Fidelis, A. Zemla, and T. Hubbard. Critical assessment of methods on protein structure prediction (CASP)-round IV. Proteins: Structure, Function and Genetics, 45(S5):2-7, December 2001.
3. J. Moult, F. Fidelis, A. Zemla, and T. Hubbard. Critical assessment of methods on protein structure prediction (CASP)-round V. Proteins: Structure, Function and Genetics, 53(S6):334-339, October 2003. (Pubitemid 37352192)
4. J.M. Bujnicki, A. Elofsson, D. Fischer, and L. Rychlewski. Livebench-2: Large-scale automated evaluation of protein structure prediction servers. Proteins: Structure, Function and Genetics, 45:184-191, 2001. (Pubitemid 34113182)
5. L. Rychlewski, D. Fischer, and A. Elofsson. Livebench-6: Large-scale evaluation of protein structure prediction servers. Proteins: Structure, Function and Genetics, 53:542-547, 2003. (Pubitemid 37352214)
6. D. Fischer, L. Rychlewski, R.L. Dunbrack, A.R. Ortiz, and A. Elofsson. CAFASP3: The third critical assessment of fully automated structure prediction methods suppl. Proteins: Structure, Function and Genetics, S6(53):503-516, October 2003. (Pubitemid 37352210)
7. D. Fischer, A. Elofsson, and L. Rychlewski. The 2000 olympic games of protein structure prediction. Protein Engineering, 13(10):667-670, October 2000.
8. J. Lundström, L. Rychlewski, J. Bunnicki, and A. Elofsson. PCONS: A neural-netwrok-based consensus predictor that improves fold recognition. Protein Science, 10:2354-2362, 2001. (Pubitemid 32988651)
9. K. Ginalski, A. Elofsson, D. Fischer, and L. Rychlewski. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19(8):1015-1018, 2003. (Pubitemid 36675823)
10. B.Wallner, H. Fang, and A. Elofsson. Automatic consensus-based fold recognition using pcons, proq, and pmodeller. Proteins: Structure, Function and Genetics, pages 534-541, 2003. (Pubitemid 37352213)
11. D. Fischer. 3DS3 and 3DS5: 3D-SHOTGUN meta-predictors in CAFASP3. Proteins: Structure, Function and Genetics, 53:517-523, 2003. (Pubitemid 37352211)
12. I. Sasson and D. Fischer. Modeling three-dimensional protein structures for CASP5 using the 3D-SHOTGUN meta-predictors. Proteins: Structure, Function and Genetics, 53:389-394, 2003. (Pubitemid 37352197)
13. D. Fischer. Hybrid fold recognition: Combining sequence derived properties with evolutionary information. pages 119-130, Hawaii, 2000. Biocomputing: Proceedings of the 2000 Pacific Symposium, World Scientific Publishing Co.
14. L.A. Kelley, R.M. MacCallum, and M.J.E. Sternberg. Enhanced genome annotation using structural profiles in the program 3D-PSSM. Journal of Molecular Biology, 299(2):499-520, 2000.
15. B. Wallner and A. Elofsson. Can correct protein models be identified ? Protein Science, 12(5):1073-1086, 2003. (Pubitemid 36505441)
16. N. Siew, A. Elofsson, L. Rychlewski, and D. Fischer. Maxsub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16(9):776-785, 2000.
17. V.N. Vapnik. The Nature of Statistical Learning Theory. Springer, 1995.
18. Alex J. Smola and Bernhard Sch lkopf. A tutorial on support vector regression. Technical report, October 1998.
19. T. Joachims. Making Large-scale SVM Learning Practical. MIT Press, 1999.
20. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystography, 26:283-291, 1993.
21. G. Vriend. WHATIF: a molecular modeling and drug design program. Journal of Molecular Graphics, 8:52-56, 1990. (Pubitemid 20717037)
22. L. Rychlewski, L. Jaroszewski, W. Li, and A. Godzik. Comparison of sequence profiles: strategies for structural predictions using sequence information. Protein Science, (9):232-241, 2000. (Pubitemid 30126996)
23. L. Jaroszewski, L. Rychlewski, and A. Godzik. Improving the quality of twilight-zone alignments. Protein Science, (9):1487-1496, 2000. (Pubitemid 30659187)
24. J. Shi, L. B. Tom, and M. Kenji. FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. Journal of Molecular Biology, 310:243-257, 2001. (Pubitemid 32619966)
25. J. Gough, K. Karplus, R. Hughey, and C. Chothia. Assignment of homology to genome sequences using a library of hidden markov models that represent all proteins of known structure. Journal of Molecular Biology, 313(4):903-919, 2001. (Pubitemid 33063435)
26. L.J. McGuffin and D.T. Jones. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, (19):874-881, 2003. (Pubitemid 36582404)