META-PP: Single interface to crucial prediction servers

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3308-3310

  Eyrich, Volker A ^a   Rost, Burkhard ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER MODEL; INTERNET; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; PHYSIOLOGY; PROTEIN CONFORMATION; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY; SYSTEM ANALYSIS;

INTERNET; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 0042121311     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg572     Document Type: Article

References (27)

1. . Moult, J., Pedersen, J.T., Judson, R. and Fidelis, K. (1995) A large-scale experiment to assess protein structure prediction methods. Proteins, 23, ii-iv.
2. Moult, J., Hubbard, T., Bryant, S.H., Fidelis ,K. and Pedersen, J.T. (1997) Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins, 29 (Suppl. 1), 2-6.
3. Moult, J., Fidelis, K., Zemla, A. and Hubbard, T. (2001) Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins, 45 (Suppl. 5), 2-7.
4. Moult, J., Hubbard, T., Bryant, S.H., Fidelis, K. and Pedersen, J.T. (1999) Critical assessment of methods of protein structure prediction (CASP): round III. Proteins, 37 (Suppl. 3), 2-6.
5. Fischer, D., Barret, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D., Karplus, K.J., Kelley, L.A., MacCallum, R.M., Pawowski, K. et al. (1999) CAFASP-1: Critical assessment of fully automated structure prediction methods. Proteins, 37, 209-217.
6. Eyrich, V.A., Marti-Renom, M.A., Przybylski, D., Madhusudhan, M.S., Fiser, A., Pazos, F., Valencia, A., Sali, A. and Rost, B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243.
7. Marti-Renom, M.A., Madhusudhan, M.S., Fiser, A., Rost, B. and Sali, A. (2002) Reliability of assessment of protein structure prediction methods. Structure, 10, 435-440.
8. Rost, B. and Eyrich, V.A. (2001) EVA: Large-scale analysis of secondary structure prediction. Proteins, 45, 192-199.
9. Rost, B. and Liu, J. (2003) The PredictProtein server. Nucleic Acids Res., 31, 3300-3304.
10. Lund, O., Frimand, K., Gorodkin, J., Bohr, H., Bohr, J., Hansen, J. and Brunak, S. (1997) Protein distance constraints predicted by neural networks and probability density functions. Protein Eng., 10, 1241-1248.
11. Emanuelsson, O., Nielsen, H. and Von Heijne, G. (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci., 8, 978-984.
12. Cuff, J.A., Clamp, M.E., Siddiqui, A.S., Finlay, M. and Barton, G.J. (1998) JPred: a consensus secondary structure prediction server. Bioinformatics, 14, 892-893.
13. Cuff, J.A. and Barton, G.J. (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 40, 502-511.
14. Hansen, J.E., Lund, O., Tolstrup, N., Gooley, A.A., Williams, K.L. and Brunak, S. (1998) NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glyco. J., 15, 115-130.
15. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
16. McGuffin, L.J., Bryson K. and Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
17. Rost, B. and Sander, C. (1993) Prediction of protein secondary structure at better than 70 percent accuracy. J. Mol. Biol., 232, 584-599.
18. Rost, B. and Sander, C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19, 55-72.
19. Karplus, K., Barrett, C. and Hughey, R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
20. Baldi, P., Brunak, S., Frasconi, P., Soda, G. and Pollastri, G. (1999) Exploiting the past and the future in protein secondary structure prediction. Bioinformatics, 15, 937-946.
21. Pollastri, G., Przybylski, D., Rost, B. and Baldi, P. (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-235.
22. Nielsen, H., Brunak, S. and von Heijne, G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng., 12, 3-9.
23. Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
24. Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
25. Guex, N., Diemand, A. and Peitsch, M.C. (1999) Protein modelling for all. Trends Biochem. Sci., 24, 364-367.
26. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E.L.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
27. Claros, M.G. and Von Heijne, G. (1994) Toppred-II - an improved software for membrane-protein structure predictions. Comp. Appl. Biosci., 10, 685-686.