메뉴 건너뛰기




Volumn , Issue , 2007, Pages 741-747

Classification of enzyme function from protein sequence based on feature representation

Author keywords

Amino acid composition; Attribute selection; Enzyme function; Feature analysis; Feature extraction; Function classification; Machine learning; Protein classificaton

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; BIOINFORMATICS; CATALYSTS; CHEMICAL REACTIONS; COMPUTER AIDED DIAGNOSIS; ENZYMES; FUNCTIONS; LEARNING SYSTEMS; ORGANIC ACIDS; PROBABILITY DENSITY FUNCTION; PROTEINS; ROBOT LEARNING; STRUCTURE (COMPOSITION);

EID: 47649089566     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375643     Document Type: Conference Paper
Times cited : (15)

References (37)
  • 1
    • 0003450992 scopus 로고    scopus 로고
    • Nomenclature Committee of the International Union of Biochemistry and Molecular Biology NC-IUBMB, Academic Press, NY
    • Enzyme-Nomenclature, Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), Academic Press, NY (http://www.chem.qmul.ac.uk/iubmb/enzyme/).
    • Enzyme-Nomenclature
  • 2
    • 0032893084 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
    • Bairoch, A. and Apweiler, R., "The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999," Nucleic Acids Research, vol. 27, pp. 49-54, 1999.
    • (1999) Nucleic Acids Research , vol.27 , pp. 49-54
    • Bairoch, A.1    Apweiler, R.2
  • 3
    • 13444251475 scopus 로고    scopus 로고
    • Predicting functional family of novel enzymes irrespective of sequence similarity
    • L.Y. Han, C.Z. Cai, Z.L. Ji, Z.W. Cao, J. Cui, and Y.Z. Chen, "Predicting functional family of novel enzymes irrespective of sequence similarity," Nucleic Acids Research, vol. 32, pp. 6437-6444, 2004.
    • (2004) Nucleic Acids Research , vol.32 , pp. 6437-6444
    • Han, L.Y.1    Cai, C.Z.2    Ji, Z.L.3    Cao, Z.W.4    Cui, J.5    Chen, Y.Z.6
  • 4
    • 0041736652 scopus 로고    scopus 로고
    • Protein function classification via support vector machine approach
    • C.Z. Cai, W.L. Wang, L.Z. Sun, and Y.Z. Chen, "Protein function classification via support vector machine approach," Mathematical Biosciences, vol. 185, pp. 111-122, 2003.
    • (2003) Mathematical Biosciences , vol.185 , pp. 111-122
    • Cai, C.Z.1    Wang, W.L.2    Sun, L.Z.3    Chen, Y.Z.4
  • 5
    • 0030623641 scopus 로고    scopus 로고
    • Predicting enzyme function from sequence: A systematic appraisal
    • Shah, I. and Hunter, L., "Predicting enzyme function from sequence: a systematic appraisal," In the proceeding of ISMB, pp. 276-283, 1999.
    • (1999) In the proceeding of ISMB , pp. 276-283
    • Shah, I.1    Hunter, L.2
  • 6
    • 0042235504 scopus 로고    scopus 로고
    • Automated data-driven discovery of motif-based protein function classifiers
    • Xiangyun Wang, Diane Schroeder, Drena Dobbs, and Vasant Honavar, "Automated data-driven discovery of motif-based protein function classifiers," Information Sciences, vol. 155, pp. 1-18, 2003.
    • (2003) Information Sciences , vol.155 , pp. 1-18
    • Wang, X.1    Schroeder, D.2    Dobbs, D.3    Honavar, V.4
  • 9
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of Function in Protein Superfamilies, from a Structural Perspective
    • Annabel E. Todd, Christine A. Orengo, and Janet M. Thornton, "Evolution of Function in Protein Superfamilies, from a Structural Perspective," J. Mol. Biol., vol. 307, pp. 1113-1143, 2001.
    • (2001) J. Mol. Biol , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 11
    • 47649109030 scopus 로고    scopus 로고
    • Enzyme function prediction with interpretable models
    • Umar Syed and Golan Yona, "Enzyme function prediction with interpretable models," Computational Systems Biology, pp. 1-33, 2007.
    • (2007) Computational Systems Biology , pp. 1-33
    • Syed, U.1    Yona, G.2
  • 12
    • 9644283060 scopus 로고    scopus 로고
    • Paul D. Dobson and Andrew J. Doig, Predicting Enzyme Class from Protein Structure without Alignments, JMB, 345, pp. 187-199, 2005.
    • Paul D. Dobson and Andrew J. Doig, "Predicting Enzyme Class from Protein Structure without Alignments," JMB, vol. 345, pp. 187-199, 2005.
  • 13
    • 4944225083 scopus 로고    scopus 로고
    • Remote homolgy detection: A motif based approach
    • Asa Ben-Hur and Douglas Brutlag, "Remote homolgy detection: a motif based approach," Bioinformatics, Vol. 19 Suppl. 1, pp. i26-i33, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Ben-Hur, A.1    Brutlag, D.2
  • 16
    • 0038038642 scopus 로고    scopus 로고
    • Using a mixture of probabilistic decision trees for direct prediction of protein function
    • U. Syed and G. Yona, "Using a mixture of probabilistic decision trees for direct prediction of protein function," RECOMB, pp 289-300, 2003.
    • (2003) RECOMB , pp. 289-300
    • Syed, U.1    Yona, G.2
  • 17
    • 13444251475 scopus 로고    scopus 로고
    • Predicting functional family of novel enzymes irrespective of sequence similarity : A statistical learning approach
    • L.Y. Han, C. Z. Cai, Z.L. Ji, Z. W. Cao, J.Cui, and Y. Z. Chen, "Predicting functional family of novel enzymes irrespective of sequence similarity : a statistical learning approach," Nucleic Acids Research, vol. 32, pp. 6437-6444, 2004.
    • (2004) Nucleic Acids Research , vol.32 , pp. 6437-6444
    • Han, L.Y.1    Cai, C.Z.2    Ji, Z.L.3    Cao, Z.W.4    Cui, J.5    Chen, Y.Z.6
  • 19
    • 0029619259 scopus 로고
    • Knowledge-Based Protein Secondary Structure Assignment
    • Dmitrij Frishman and Patrick Argos, "Knowledge-Based Protein Secondary Structure Assignment," Proteins: Structure, Function, and Genetics, vol. 23, pp. 566-579, 1995.
    • (1995) Proteins: Structure, Function, and Genetics , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 20
    • 33745561205 scopus 로고    scopus 로고
    • An Introduction to Variable and Feature Selection
    • Isabelle Guyon, "An Introduction to Variable and Feature Selection," Journal of Machine Learning Research, vol. 3, pp. 1157-1182, 2003.
    • (2003) Journal of Machine Learning Research , vol.3 , pp. 1157-1182
    • Guyon, I.1
  • 21
    • 47649120761 scopus 로고    scopus 로고
    • J. Ross Quinlan, C4.5: programs for machine learning, San Francisco, Morgan Kaufmann, 1993.
    • J. Ross Quinlan, C4.5: programs for machine learning, San Francisco, Morgan Kaufmann, 1993.
  • 22
    • 68549121111 scopus 로고    scopus 로고
    • C4.5 and Imbalanced Data sets: Investigating the effect of sampling method, probabilistic estimate, and decision tree structure
    • Nitesh V. Chawla, "C4.5 and Imbalanced Data sets: Investigating the effect of sampling method, probabilistic estimate, and decision tree structure," Workshop on Learning from Imbalanced Datasets II, ICML, 2003.
    • (2003) Workshop on Learning from Imbalanced Datasets II, ICML
    • Chawla, N.V.1
  • 23
    • 0036892449 scopus 로고    scopus 로고
    • Prediction of novel archaeal enzymes from sequence-derived features
    • Lars Juhl Jensen, Marie Skovgaard, and Soren Brunak, "Prediction of novel archaeal enzymes from sequence-derived features," Protein Science, vol. 3, pp. 2894-2898, 2002.
    • (2002) Protein Science , vol.3 , pp. 2894-2898
    • Juhl Jensen, L.1    Skovgaard, M.2    Brunak, S.3
  • 24
    • 33749078148 scopus 로고    scopus 로고
    • Luiz C. Borro, Stanley R.M. Oliveira, Michel E.B. Yamagishi, Adaulto L. Mancini, Jose G. Jardine, Ivan Mazoni, Edgard H. dos Santos, Roberto H. Higa, Paula R. Kuser, and Goran Neshich, Predicting enzyme class from protein structure using Bayesian classification, Genetics and Molecular Research, 5, pp. 193-202, 2006.
    • Luiz C. Borro, Stanley R.M. Oliveira, Michel E.B. Yamagishi, Adaulto L. Mancini, Jose G. Jardine, Ivan Mazoni, Edgard H. dos Santos, Roberto H. Higa, Paula R. Kuser, and Goran Neshich, "Predicting enzyme class from protein structure using Bayesian classification," Genetics and Molecular Research, vol. 5, pp. 193-202, 2006.
  • 27
    • 0025821131 scopus 로고
    • Characterization of a heat-stable NADP-dependent isocitrate dehydrogenase from the obligate thermophile Thermoleophilum minutum YS-4
    • James F. Novotny Jr. and Jerome J. Perry, "Characterization of a heat-stable NADP-dependent isocitrate dehydrogenase from the obligate thermophile Thermoleophilum minutum YS-4," Applied Microbiology and Biotechnology, vol. 35, 1991.
    • (1991) Applied Microbiology and Biotechnology , vol.35
    • Novotny Jr., J.F.1    Perry, J.J.2
  • 28
    • 33644630561 scopus 로고    scopus 로고
    • FRANKSUM: New feature selection method for protein funciton prediction
    • Ali Al-Shahib, Rainer Breitling, and David Gilbert, "FRANKSUM: New feature selection method for protein funciton prediction," International Journal of Neural Systems, vol. 15, pp. 250-275, 2005.
    • (2005) International Journal of Neural Systems , vol.15 , pp. 250-275
    • Al-Shahib, A.1    Breitling, R.2    Gilbert, D.3
  • 35
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition
    • Kuo-Chen Chou, "Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition," Proteins: Sturcture, Function, and Genetics vol.43, pp. 246-255, 2001.
    • (2001) Proteins: Sturcture, Function, and Genetics , vol.43 , pp. 246-255
    • Chou, K.-C.1
  • 36
    • 12744279642 scopus 로고    scopus 로고
    • Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    • Chou, K.C., "Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes," Bioinformataics, vol. 21, pp. 10-19, 2005.
    • (2005) Bioinformataics , vol.21 , pp. 10-19
    • Chou, K.C.1
  • 37
    • 27344448597 scopus 로고    scopus 로고
    • Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence
    • Ali Al-Shahib, Rainer Breitling, and David Gilbert, "Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence," Appl Bioinformatics, vol. 4, pp. 195-203, 2005.
    • (2005) Appl Bioinformatics , vol.4 , pp. 195-203
    • Al-Shahib, A.1    Breitling, R.2    Gilbert, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.