Prediction of outer membrane proteins by support vector machines using combinations of gapped amino acid pair compositions

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 113-120

  Huang, Ssu Hua ^a   Liu, Ru Sheng ^a   Chen, Chien Yu ^a   Chao, Ya Ting ^a   Chen, Shu Yuan ^a  

^a YUAN ZE UNIVERSITY   (Taiwan)

Author keywords

barrel membrane proteins; Gapped amino acid pair composition; Outer membrane protein prediction; Support vector machine

Indexed keywords

AMINO ACIDS; CELL MEMBRANES; COMPUTATIONAL METHODS; DATA STRUCTURES; LEARNING SYSTEMS; MOLECULAR STRUCTURE;

DATASETS; GAPPED AMINO ACID PAIR COMPOSITION; GLOBULAR PROTEINS; OUTER MEMBRANE PROTEINS; SUPPORT VECTOR MACHINES;

PROTEINS;

EID: 33751183057     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.48     Document Type: Conference Paper

References (15)

1. Martelli, P.L., Fariselli, P., Krogh, A. and Casadio, R., "A Sequence-Profile-Based HMM for Predicting and Discriminating β Barrel Membrane Proteins", Bioinformatics, 18, 2002, pp. S46-S53.
2. Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C. and Hamodrakas, S.J., "A Hidden Markov Model Method, Capable of Predicting and Discriminating β-Barrel Outer Membrane Proteins", BMC Bioinformatics, 5, 2004, pp. 29, the web service at: http://bioinformatics.biol.uoa.gr/ PRED-TMBB.
3. Bigelow, H.R., Petrey, D.S., Liu, J., Przybylski, D. and Rost, B., "Predicting Transmembrane Beta-Barrels in Proteomes", Nucleic Acids Research, 32, 2004, pp. 2566-2577.
4. Liu, Q., Zhu, Y., Wang, B. and Li, Y., "Identification of β-Barrel Membrane Proteins Based on Amino Acid Composition Properties and Predicted Secondary Structure", Computational Biology and Chemistry, 27, 2003, pp. 355-361.
5. She, R., Chen, F., Wang, K., Ester, M., Gardy, J.L. and Brinkman, F.S.L., "Frequent-Subsequence-Based Prediction of Outer Membrane Proteins", SIGKDD'03, August 2003, pp. 24-27.
6. Gardy, J.L., Laird, M.R., Chen, F., Rey, S., Walsh, C. J., Ester, M. and Brinkman, F.S.L., "PSORTb v.2.0: Expanded Prediction of Bacterial Protein Subcellular Localization and Insights Gained from Comparative Proteome Analysis", Bioinformatics, 21, 2005, pp. 617-623.
7. Gromiha, M.M. and Suwa, M., "A Simple Statistical Method for Discriminating Outer Membrane Proteins with Better Accuracy", Bioinformatics, 21, 2005, pp. 961-968.
8. Gromiha, M.M., Ahmad, S. and Suwa, M., "Application of Residue Distribution along the Sequence for Discriminating Outer Membrane Proteins", Computational Biology and Cheminstry, 29, 2005, pp. 135-142.
9. Zhai, Y. and Saier, M., "The β-Barrel Finder (BBF) Program, Allowing Identification of Outer Membrane β-Barrel Proteins Encoded within Prokaryotic Genomes", Protein Science, 11, 2002, pp. 2196-2207.
10. Berven, F.S., Flikka, K., Jensen, H.B. and Eidhammer, I., "BOMP: a Program to Predict Integral β-Barrel Outer Membrane Proteins Encoded within Genomes of Gram-Negative Bacteria", Nucleic Acids Research, 32, 2004, pp. W394-W399.
11. Hua, S. and Sun, Z., "Support Vector Machine Approach for Protein Subcellular Localization Prediction", Bioinformatics, 17, 2001, pp. 721-728.
12. Park, K.-J., and Kanehisa, M., "Prediction of Protein Subcellular Localizations by Support Vector Machines Using Compositions of Amino Acids and Amino Acid Pairs", Bioinformatics, 19, 2003, pp. 1656-1663.
13. Guo, J., Lin, Y. and Sun, Z., "A Novel Method for Protein Subcellular Localization: Combining Residue-Couple Model and SVM", Proceedings of The 3rd Asia-Pacific Bioinformatics Conference, January 2005, pp. 117-129.
14. Gardy, J.L., Spencer, C., Wang, K., Ester, M., Tusnady, G.E., Simon, I., Hua, S., deFays, K., Lambert, C., Nakai, K. and Brinkman, F.S.L., "PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria", Nucleic Acids Research, 31, 2003, pp. 3613-17.
15. Chang, C.-C. and Lin, C.-J., "LIBSVM: A Library for Support Vector Machines", 2001. Software available at http://www.csie.ntu.edu.tw/~cjlin/ libsvm.