Pattern analysis for the prediction of fungal pro-peptide cleavage sites

Discrete Applied Mathematics

Volumn 157, Issue 10, 2009, Pages 2388-2394

  Ozogur Akyuz S ^a   Shawe Taylor, J ^b   Weber, G W ^a   Ogel Z B ^a  

^a MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Computational biology; Continuous optimization; LibSVM; Machine learning; Pro peptide cleavage site; Support vector machines

Indexed keywords

COMPUTATIONAL BIOLOGY; CONTINUOUS OPTIMIZATION; LIBSVM; MACHINE LEARNING; PRO-PEPTIDE CLEAVAGE SITE;

APPLICATIONS; BIOINFORMATICS; GENE EXPRESSION; IMAGE RETRIEVAL; MULTILAYER NEURAL NETWORKS; PROTEINS; ROBOT LEARNING; SUPPORT VECTOR MACHINES;

AMINES;

EID: 67349206442     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dam.2008.06.043     Document Type: Article

References (33)

1. Altschul S.F. Amino acid substitution matrices from an information theoretic perspective. Journal of Molecular Biology 219 (1991) 555-665
2. Atalay V., and Cetin-Atalay R. Implicit motif distribution based hybrid computational kernel for sequence classification. Bioinformatics 21 8 (2005) 1429-1436
3. Baker D., Shiau A.K., and Agard D.A. The role of pro regions in protein folding. Current Opinion in Cell Biology 5 6 (1993) 966-970 (Review)
4. Bendtsen J.D., Nielsen H., Heijne G., and Brunak S. Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology 340 (2004) 783-795
5. Cristianini N., and Shawe-Taylor J. An Introduction to Support Vector Machines and other Kernel-Based Learning Methods (2000), Cambridge University Press
6. Cai Y.-D., Liub X.-J., Xu X.-B., and Chou K.-C. Prediction of protein structural classes by support vector machines. Computers and Chemistry 26 (2002) 293-296
7. Cai Y.-D., Lin S.-L., and Chou K.-C. Support vector machines for prediction of protein signal sequences and their cleavage sites. Peptides 24 (2003) 159-161
8. C.-C. Chang, C.-J. Lin, LIBSVM: a library for support vector machines, 2001. Software available at: http://www.csie.ntu.edu.tw/cjlin/libsvm
9. Chou K.-C. Prediction of signal peptides using scaled window. Peptides 22 (2001) 1973-1979
10. Claros M.G., Brunak S., and von Heijne G. Prediction of N-terminal protein sorting signals. Current Opinion in Structural Biology 7 (1997) 394-398
11. Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: M.O. D. (Ed). Atlas of Protein Sequence and Structure, vol. 5 (3) (1978), National Biomedical Research Foundation, Washington 345-352
12. Dubey A., Realff M.J., Lee J.H., and Bommarius A.S. Support vector machines for learning to identify the critical positions of a protein. Journal of Theoretical Biology 234 (2005) 351-361
13. Duckert P., Brunak S., and Blom N. Prediction of proprotein convertase cleavage sites. Protein Engineering, Design and Selection 17 1 (2004) 107-112
14. Evin G., Zhu A., Holsinger R.M.D., Masters C.L., and Li Q.-X. Proteolytic processing of the Alzheimers's disease amyloid precursor protein in brain and platelets. Journal of Neuroscience Research 74 (2003) 386-392
15. Hastie T., Tibshirani R., and Friedman J. The Elements of Statistical Learning - Data Mining, Inference and Prediction. Springer Series in Statistics (2001)
16. R. Jalving, Proteolytic processing in the secretory pathways of Aspergillus niger, Ph.D. Thesis, Wageningen University, 2005
17. Jeenes D.J., Mackenzie D.A., Roberts I.N., and Archer D.B. Heterologous protein production by filamentous fungi. Biotechnology and Genetic Engineering Reviews 9 (1991) 327-367
18. Kawashima S., Ogata H., and Kanehisa M. AAindex: Amino acid index database. Nucleic Acids Research 27 (1999) 368-369
19. Nevalainen K.M.H., Te'o V.S.J., and Bergquist P.L. Heterologous protein expression in filamentous fungi. Trends in Biotechnology 23 9 (2005) 468-474
20. H. Nicholas, A. Ropelewski, Sequence analysis: Which scoring method should I use? http://www.psc.edu/research/biomed/homologous/scoring_primer.html
21. Nielsen H., Engelbrecht J., Brunak S., and von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 10 (1997) 1-6
22. Z.B. Ögel, Molecular analysis of a fungal galactose oxidase gene, Ph.D. Thesis, Univ. of Leeds, Leeds, UK, 1993
23. Punt P.J., van Biezen N., Conesa A., Albers A., Mangnus J., and van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends in Biotechnology 20 5 (2002) 200-2006
24. Punt P.J., Drint-Kuijvenhoven A., Lokman B.C., Spencer J.A., Jeenes D., Archer D.A., and van den Hondel C.A. The role of the Aspergillus niger furin-type protease gene in processing of fungal proproteins and fusion proteins. Evidence for alternative processing of recombinant (fusion-) proteins. Journal of Biotechnology 5 106 1 (2003) 23-32
25. Shinde U.P., Liu J.J., and Inouye M. Protein memory through altered folding mediated by intramolecular chaperones. Nature 389 6650 (1997) 520-522
26. Shawe-Taylor J. Classification Accuracy based on observed margin. Algorithmica 22 (1998) 157-172
27. Shawe-Taylor J., and Cristianini N. Kernel Methods for Pattern Analysis (2004), Cambridge University Press pp. 344-396
28. Shawe-Taylor J. Neural Network Learning: Theoretical Foundations (2001), Cambridge University Press (Review of Anthony, Martin; Bartlett, Peter L.)
29. Spiro R.G. Protein glycosylation: Nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12 4 (2002) 43R-56R (Review)
30. Springael J.Y., Nikko E., André B., and Marini A.M. Yeast Npi3/Bro1 is involved in ubiquitin-dependent control of permease trafficking. FEBS Letters 517 (2002) 103-109
31. Steinwart I. On the influence of the kernel on the consistency of support vector machines. Journal of Machine Learning Research 2 (2001) 67-93
32. Von Heijne G. A new method for predicting signal sequence cleavage sites. Nucleic Acids Research 14 1 (1986) 4683-4690
33. Weidemann A., Paliga K., Dürrwang U., Reinhard F.B.M., Schuckert O., Evin G., and Masters C.L. Proteolytic processing of the alzheimers disease amyloid precursor protein within its cytoplasmic domain by caspase-like proteases. The Journal of Biological Chemistry 274 9 26 (1999) 5823-5829