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Volumn 3, Issue 3, 2011, Pages 239-250

Improved protein secondary structure prediction using a intelligent HSVM method with a new encoding scheme

Author keywords

Encoding scheme; HSVM; Protein secondary structure prediction

Indexed keywords

AMINO ACID RESIDUES; BLIND TEST; COGNITIVE MECHANISMS; COMPOUND PYRAMID MODELS; DATA SETS; ENCODING SCHEMES; EVOLUTIONARY INFORMATION; GENERALIZATION ABILITY; HSVM; HYBRID METHOD; KNOWLEDGE DISCOVERY; MULTI-LAYERED; PHYSICOCHEMICAL PROPERTY; PREDICTION PROCESS; PREDICTION SYSTEMS; PROTEIN SECONDARY STRUCTURE; PROTEIN SECONDARY STRUCTURE PREDICTION; SECONDARY STRUCTURE PREDICTION; SECONDARY STRUCTURES; SEQUENCE ANALYSIS; TERTIARY STRUCTURES;

EID: 79956219935     PISSN: 20058039     EISSN: None     Source Type: Journal    
DOI: 10.4156/ijact.vol3.issue3.24     Document Type: Article
Times cited : (9)

References (45)
  • 1
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., Sander C., Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol. 22, no. 12, pp.2577-637, 1983.
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 2
    • 84995046262 scopus 로고
    • A large-scale experiment to assess protein structure prediction methods
    • Moult, J., et al, A large-scale experiment to assess protein structure prediction methods, Proteins: Structure Function Genetics vol. 23, no. 3, pp. 2-4, 1995.
    • (1995) Proteins: Structure Function Genetics , vol.23 , Issue.3 , pp. 2-4
    • Moult, J.1
  • 3
    • 0043123211 scopus 로고    scopus 로고
    • EVA: Evaluation of protein structure prediction servers
    • Koh, I. Y., V. A. Eyrich, et al, EVA: Evaluation of protein structure prediction servers, Nucleic Acids Res, vol. 31, no. 13, pp. 3311-3315, 2003.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3311-3315
    • Koh, I.Y.1    Eyrich, V.A.2
  • 4
    • 0029874551 scopus 로고    scopus 로고
    • Protein fold recognition using sequence-derived predictions
    • Fischer, D. and Eisenberg, D, Protein fold recognition using sequence-derived predictions, Protein Sci., vol. 5, pp. 947-955, 1996.
    • (1996) Protein Sci , vol.5 , pp. 947-955
    • Fischer, D.1    Eisenberg, D.2
  • 5
    • 0028158628 scopus 로고
    • PHD-an automatic mail server for protein secondary structure prediction
    • Rost B, Sander C, Schneider R, PHD-an automatic mail server for protein secondary structure prediction, Comput Appl Biosci, vol. 10, pp. 53-60, 1994.
    • (1994) Comput Appl Biosci , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 6
    • 0037818341 scopus 로고    scopus 로고
    • Local structure prediction with local structure-based sequence profiles
    • Yang, A.S. and Wang, L.Y, Local structure prediction with local structure-based sequence profiles, Bioinformatics, vol. 19, pp. 1267-1274, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 1267-1274
    • Yang, A.S.1    Wang, L.Y.2
  • 7
    • 0037661371 scopus 로고    scopus 로고
    • Benchmarking secondary structure prediction for fold recognition
    • McGuffin, L.J. and Jones, D.T, Benchmarking secondary structure prediction for fold recognition, Proteins, vol. 52, pp. 166-175, 2003.
    • (2003) Proteins , vol.52 , pp. 166-175
    • McGuffin, L.J.1    Jones, D.T.2
  • 8
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T, Protein secondary structure prediction based on position-specific scoring matrices, J. Mol. Biol., vol. 292, pp. 195-202, 1999.
    • (1999) J. Mol. Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 9
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin, L.J., Bryson, K. and Jones, D.T, The PSIPRED protein structure prediction server, Bioinformatics, vol. 16, 404-405, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 10
    • 0023803244 scopus 로고
    • Predicting the secondary structure of globular proteins using neural network models
    • Qian N, Sejnowski T J, Predicting the secondary structure of globular proteins using neural network models, Journal of Molecular Biology, vol. 202, pp. 865-884, 1988.
    • (1988) Journal of Molecular Biology , vol.202 , pp. 865-884
    • Qian, N.1    Sejnowski, T.J.2
  • 11
    • 0242362161 scopus 로고    scopus 로고
    • Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
    • Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R, Combining local-structure, fold-recognition, and new fold methods for protein structure prediction, Proteins, vol. 53, no. 6, pp. 491-496, 2003.
    • (2003) Proteins , vol.53 , Issue.6 , pp. 491-496
    • Karplus, K.1    Karchin, R.2    Draper, J.3    Casper, J.4    Mandel-Gutfreund, Y.5    Diekhans, M.6    Hughey, R.7
  • 12
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
    • Hua S, Sun Z, A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach, J Mol Biol., vol. 308, no. 2, pp. 397-407, 2001.
    • (2001) J Mol Biol , vol.308 , Issue.2 , pp. 397-407
    • Hua, S.1    Sun, Z.2
  • 14
    • 33745582911 scopus 로고    scopus 로고
    • Bioinformatics and data mining in proteomics
    • Haoudi H Bensmail, Bioinformatics and data mining in proteomics, Expert Review of Proteomics, vol. 3, no. 3, pp. 333-343, 2006.
    • (2006) Expert Review of Proteomics , vol.3 , Issue.3 , pp. 333-343
    • Bensmail, H.H.1
  • 15
    • 19344378239 scopus 로고    scopus 로고
    • Protein secondary structure prediction using dynamic programming
    • Jing Zhao, Pei-Ming Song, Qing Fang and Jian-Hua Luo, Protein secondary structure prediction using dynamic programming, Acta Biochimica et Biophysica Sinica, vol. 37, no. 3, pp.167-172, 2005.
    • (2005) Acta Biochimica Et Biophysica Sinica , vol.37 , Issue.3 , pp. 167-172
    • Zhao, J.1    Song, P.-M.2    Fang, Q.3    Luo, J.-H.4
  • 16
    • 0036520412 scopus 로고    scopus 로고
    • Ming Quantitative association rules with standard SQL queries and it's evaluation
    • Bingru, Yang, Haihong, Sun, and Fanlun, Xiong, Ming Quantitative association rules with standard SQL queries and it's evaluation, Journal of Computer Research and Development, vol. 39, no. 3, pp. 307-312, 2002.
    • (2002) Journal of Computer Research and Development , vol.39 , Issue.3 , pp. 307-312
    • Bingru, Y.1    Haihong, S.2    Fanlun, X.3
  • 17
    • 0033106244 scopus 로고    scopus 로고
    • Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
    • Cuff J. A. and Barton G. J, Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins: Structure, Function and Genet, vol. 34, pp. 508-519, 1999.
    • (1999) Proteins: Structure, Function and Genet , vol.34 , pp. 508-519
    • Cuff, J.A.1    Barton, G.J.2
  • 18
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost B, Sander C, Prediction of protein secondary structure at better than 70% accuracy, J Mol Biol 232(2) (1993) 584-99.
    • (1993) J Mol Biol , vol.232 , Issue.2 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 19
    • 0033081846 scopus 로고    scopus 로고
    • A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment
    • Zemla A, Venclovas C, Fidelis K, Rost B, A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment, Proteins, vol. 34, no. 2, pp. 220-223, 1999.
    • (1999) Proteins , vol.34 , Issue.2 , pp. 220-223
    • Zemla, A.1    Venclovas, C.2    Fidelis, K.3    Rost, B.4
  • 20
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignment profiles to improve rotein secondary structure prediction
    • Cuff J.A. and Barton, G.J, Application of multiple sequence alignment profiles to improve rotein secondary structure prediction, Proteins, vol. 40, pp. 502-511, 2000.
    • (2000) Proteins , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 25
    • 20744440509 scopus 로고    scopus 로고
    • Identification of Transcription Factor Binding Sites with Variable-order Bayesian Networks
    • Ben-Gal I, Shani A, Gohr A, Grau J, Arviv S, Shmilovici A, Posch S, Grosse I, Identification of Transcription Factor Binding Sites with Variable-order Bayesian Networks, Bioinformatics, vol. 21, no. 11, pp. 2657-2666, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2657-2666
    • Ben-Gal, I.1    Shani, A.2    Gohr, A.3    Grau, J.4    Arviv, S.5    Shmilovici, A.6    Posch, S.7    Grosse, I.8
  • 26
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton, J. C. and S. Federhen, Analysis of compositionally biased regions in sequence databases, Methods Enzymol, vol. 266, pp. 554-571, 1996.
    • (1996) Methods Enzymol , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 27
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. & Henikoff, J. G, Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci USA, vol. 89, no. 22, pp. 10915-10919, 1992.
    • (1992) Proc. Natl. Acad. Sci USA , vol.89 , Issue.22 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 28
    • 0042656120 scopus 로고    scopus 로고
    • ACM SIGKDD Explorations Newsletter, ACM New York, NY, USA
    • Mannila, H. (2000), Theoretical Frameworks for Data Mining. ACM SIGKDD Explorations Newsletter, ACM New York, NY, USA, vol.1, no. 2, pp. 30-32, 2000.
    • (2000) Theoretical Frameworks For Data Mining , vol.1 , Issue.2 , pp. 30-32
    • Mannila, H.1
  • 29
    • 70350778619 scopus 로고    scopus 로고
    • New Construction of Expert System based on Knowledge Discovery
    • Bingru, Yang, Wei, Song, & Zhangyan, Xu, New Construction of Expert System based on Knowledge Discovery, Science in China Series F, vol. 37, no. 6, pp. 738-747, 2007.
    • (2007) Science In China Series F , vol.37 , Issue.6 , pp. 738-747
    • Bingru, Y.1    Wei, S.2    Zhangyan, X.3
  • 31
    • 60849135389 scopus 로고    scopus 로고
    • KAAPRO: An approach of protein secondary structure prediction based on KDD* in the compound pyramid prediction model
    • Yang Bingru, Hou Wei, et al, KAAPRO: An approach of protein secondary structure prediction based on KDD* in the compound pyramid prediction model, Expert Systems with Applications, vol. 36, no. 5, pp. 9000-9006, 2009.
    • (2009) Expert Systems With Applications , vol.36 , Issue.5 , pp. 9000-9006
    • Bingru, Y.1    Wei, H.2
  • 32
    • 70449393903 scopus 로고    scopus 로고
    • In Proceedings of the 21st Annual international Conference on Chinese Control and Decision Conference, IEEE Press, Piscataway, NJ
    • Zhun, Z., Bingru, Y., and Wei, H., An improved CBA prediction algorithm in compound pyramid model, In Proceedings of the 21st Annual international Conference on Chinese Control and Decision Conference, IEEE Press, Piscataway, NJ, pp. 5212-5216, 2009.
    • (2009) An Improved CBA Prediction Algorithm In Compound Pyramid Model , pp. 5212-5216
    • Zhun, Z.1    Bingru, Y.2    Wei, H.3
  • 33
    • 0034843744 scopus 로고    scopus 로고
    • Support vector machine approach for protein subcellular localization prediction
    • Hua SJ and Sun ZR., Support vector machine approach for protein subcellular localization prediction, Bioinformatics, vol. 17, pp. 721-728, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 721-728
    • Hua, S.J.1    Sun, Z.R.2
  • 34
    • 0141593924 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on an improved support vector machines approach
    • Hyunsoo Kim and Haesun Park, Protein secondary structure prediction based on an improved support vector machines approach, Protein Engineering, vol. 16, no. 8, pp. 553-560, 2003.
    • (2003) Protein Engineering , vol.16 , Issue.8 , pp. 553-560
    • Kim, H.1    Park, H.2
  • 36
    • 0033933636 scopus 로고    scopus 로고
    • Cascaded multiple classifiers for secondary structure prediction
    • Ouali M, King R, Cascaded multiple classifiers for secondary structure prediction, Protein Sci., vol. 9, pp. 1162-1176, 2000.
    • (2000) Protein Sci. , vol.9 , pp. 1162-1176
    • Ouali, M.1    King, R.2
  • 37
    • 0032420333 scopus 로고    scopus 로고
    • JPRED: A consensus secondary structure prediction server
    • Cuff J, Clamp M, Siddiqui A, Finlay M, Barton G, JPRED: A consensus secondary structure prediction server, Bioinformatics, vol. 14, pp. 892-893, 1998.
    • (1998) Bioinformatics , vol.14 , pp. 892-893
    • Cuff, J.1    Clamp, M.2    Siddiqui, A.3    Finlay, M.4    Barton, G.5
  • 38
    • 0030931336 scopus 로고    scopus 로고
    • 75% accuracy in protein secondary structure prediction
    • Frishman D, Argos P, 75% accuracy in protein secondary structure prediction, Proteins, vol. 27, pp. 329-335, 1997.
    • (1997) Proteins , vol.27 , pp. 329-335
    • Frishman, D.1    Argos, P.2
  • 40
    • 79956205149 scopus 로고    scopus 로고
    • Behairpred
    • Behairpred(http://www.imtech.res.in/raghava/bhairpred/)
  • 41
    • 79956213037 scopus 로고    scopus 로고
    • APSSP2
    • APSSP2(http://www.imtech.res.in/raghava/apssp2/).
  • 42
    • 79952559699 scopus 로고    scopus 로고
    • Study on source of classification in imbalanced datasets based on new ensemble classifier
    • ZHAI Yun, YANG Bing-ru, QU Wu, SUI Hai-feng, Study on source of classification in imbalanced datasets based on new ensemble classifier, Journal of Systems Engineering and Electronics, vol. 33, no. 1, pp. 196-201, 2011.
    • (2011) Journal of Systems Engineering and Electronics , vol.33 , Issue.1 , pp. 196-201
    • Yun, Z.1    Yang, B.2    Qu, W.3    Hai-Feng, S.4
  • 43
    • 79952372090 scopus 로고    scopus 로고
    • Artificial Immune System for Protein Folding Model
    • Yudong Zhang, Shuihua Wang, Lenan Wu, Yuankai Huo, Artificial Immune System for Protein Folding Model, JCIT, Vol. 6, No. 1, pp. 55-61, 2011.
    • (2011) JCIT , vol.6 , Issue.1 , pp. 55-61
    • Zhang, Y.1    Wang, S.2    Lenan, W.3    Huo, Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.