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Volumn 7, Issue 6, 2012, Pages

Accurate prediction of protein structural class

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84862521440     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037653     Document Type: Article
Times cited : (16)

References (41)
  • 1
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 3
    • 44349134514 scopus 로고    scopus 로고
    • SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences
    • Kurgan L, Cios K, Chen K, (2008) SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. BMC Bioinformatics 9: 226.
    • (2008) BMC Bioinformatics , vol.9 , pp. 226
    • Kurgan, L.1    Cios, K.2    Chen, K.3
  • 4
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR, (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33: D501-504.
    • (2005) Nucleic Acids Res , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 5
    • 0001040367 scopus 로고
    • An algorithm for protein secondary structure prediction based on class prediction
    • Deleage G, Roux B, (1987) An algorithm for protein secondary structure prediction based on class prediction. Protien Eng 1: 289-294.
    • (1987) Protien Eng , vol.1 , pp. 289-294
    • Deleage, G.1    Roux, B.2
  • 6
    • 34948846599 scopus 로고    scopus 로고
    • PreSSAPro: a software for the prediction of secondary structure by amino acid properties
    • Costantini S, Colonna G, Facchiano AM, (2007) PreSSAPro: a software for the prediction of secondary structure by amino acid properties. Comput Biol Chem 31: 389-392.
    • (2007) Comput Biol Chem , vol.31 , pp. 389-392
    • Costantini, S.1    Colonna, G.2    Facchiano, A.M.3
  • 7
    • 0022631926 scopus 로고
    • The folding type of a protein is relevant to the amino acid composition
    • Nakashima H, Nishikawa K, Ooi T, (1986) The folding type of a protein is relevant to the amino acid composition. J Biochem 99: 153-162.
    • (1986) J Biochem , vol.99 , pp. 153-162
    • Nakashima, H.1    Nishikawa, K.2    Ooi, T.3
  • 8
    • 0029051959 scopus 로고
    • A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space
    • Chou KC, (1995) A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 21: 319-344.
    • (1995) Proteins , vol.21 , pp. 319-344
    • Chou, K.C.1
  • 9
    • 0030955263 scopus 로고    scopus 로고
    • Understanding the recognition of protein structural classes by amino acid composition
    • Bahar I, Atilgan AR, Jernigan RL, Erman B, (1997) Understanding the recognition of protein structural classes by amino acid composition. Proteins 29: 172-185.
    • (1997) Proteins , vol.29 , pp. 172-185
    • Bahar, I.1    Atilgan, A.R.2    Jernigan, R.L.3    Erman, B.4
  • 10
    • 0033554601 scopus 로고    scopus 로고
    • A key driving force in determination of protein structural classes
    • Chou KC, (1999) A key driving force in determination of protein structural classes. Biochem Biophys Res Commun 264: 216-224.
    • (1999) Biochem Biophys Res Commun , vol.264 , pp. 216-224
    • Chou, K.C.1
  • 11
    • 33845338429 scopus 로고    scopus 로고
    • Using Bagging classifier to predict protein domain structural class
    • Dong L, Yuan Y, Cai Y, (2006) Using Bagging classifier to predict protein domain structural class. J Biomol Struct Dyn 24: 239-242.
    • (2006) J Biomol Struct Dyn , vol.24 , pp. 239-242
    • Dong, L.1    Yuan, Y.2    Cai, Y.3
  • 12
    • 0026632379 scopus 로고
    • Predicting protein secondary structure content: a tandem neural network approach
    • Muska SM, Kim SH, (1992) Predicting protein secondary structure content: a tandem neural network approach. J Mol Biol 255: 713-727.
    • (1992) J Mol Biol , vol.255 , pp. 713-727
    • Muska, S.M.1    Kim, S.H.2
  • 13
    • 47549084414 scopus 로고    scopus 로고
    • Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes
    • Xiao X, Lin WZ, Chou KC, (2008) Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. J Comput Chem 29: 2018-2024.
    • (2008) J Comput Chem , vol.29 , pp. 2018-2024
    • Xiao, X.1    Lin, W.Z.2    Chou, K.C.3
  • 14
    • 67650739405 scopus 로고    scopus 로고
    • Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis
    • Li ZC, Zhou XB, Dai Z, Zou XY, (2009) Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis. Amino Acids 37: 415-425.
    • (2009) Amino Acids , vol.37 , pp. 415-425
    • Li, Z.C.1    Zhou, X.B.2    Dai, Z.3    Zou, X.Y.4
  • 15
    • 0036051172 scopus 로고    scopus 로고
    • Prediction of protein structural class by amino acid and polypeptide composition
    • Luo RY, Feng ZP, Liu JK, (2002) Prediction of protein structural class by amino acid and polypeptide composition. Eur J Biochem 269: 4219-4225.
    • (2002) Eur J Biochem , vol.269 , pp. 4219-4225
    • Luo, R.Y.1    Feng, Z.P.2    Liu, J.K.3
  • 16
    • 58849136179 scopus 로고    scopus 로고
    • Prediction of the protein structural class by specific peptide frequencies
    • Costantini S, Facchiano AM, (2009) Prediction of the protein structural class by specific peptide frequencies. Biochimie 91: 226-229.
    • (2009) Biochimie , vol.91 , pp. 226-229
    • Costantini, S.1    Facchiano, A.M.2
  • 17
    • 0000520412 scopus 로고    scopus 로고
    • Prediction of protein (domain) structural classes based on amino-acid index
    • Bu WS, Feng ZP, Zhang Z, Zhang CT, (1999) Prediction of protein (domain) structural classes based on amino-acid index. Eur J Biochem 266: 1043-1049.
    • (1999) Eur J Biochem , vol.266 , pp. 1043-1049
    • Bu, W.S.1    Feng, Z.P.2    Zhang, Z.3    Zhang, C.T.4
  • 18
    • 33644889341 scopus 로고    scopus 로고
    • Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor
    • Xiao X, Shao SH, Huang ZD, Chou KC, (2006) Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor. Journal of Computational Chemistry 27: 478-482.
    • (2006) Journal of Computational Chemistry , vol.27 , pp. 478-482
    • Xiao, X.1    Shao, S.H.2    Huang, Z.D.3    Chou, K.C.4
  • 19
    • 3843117638 scopus 로고    scopus 로고
    • Predicting protein structural class by functional domain composition
    • Chou KC, Cai YD, (2004) Predicting protein structural class by functional domain composition. Biochem Biophys Res Commun 321: 1007-1009.
    • (2004) Biochem Biophys Res Commun , vol.321 , pp. 1007-1009
    • Chou, K.C.1    Cai, Y.D.2
  • 20
    • 77957124553 scopus 로고    scopus 로고
    • Prediction of protein structural class for low-similarity sequences using support vector machine and PSI-BLAST profile
    • Liu TG, Zheng XQ, Wang J, (2010) Prediction of protein structural class for low-similarity sequences using support vector machine and PSI-BLAST profile. Biochimie 92: 1330-1334.
    • (2010) Biochimie , vol.92 , pp. 1330-1334
    • Liu, T.G.1    Zheng, X.Q.2    Wang, J.3
  • 21
    • 84862773713 scopus 로고    scopus 로고
    • Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles
    • Liu T, Geng X, Zheng X, Li R, Wang J, (2011) Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles. Amino Acids.
    • (2011) Amino Acids
    • Liu, T.1    Geng, X.2    Zheng, X.3    Li, R.4    Wang, J.5
  • 22
    • 75149123557 scopus 로고    scopus 로고
    • Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences
    • Mizianty MJ, Kurgan L, (2009) Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. BMC Bioinformatics 10: 414.
    • (2009) BMC Bioinformatics , vol.10 , pp. 414
    • Mizianty, M.J.1    Kurgan, L.2
  • 23
    • 77956623830 scopus 로고    scopus 로고
    • A high-accuracy protein structural class prediction algorithm using predicted secondary structural information
    • Liu T, Jia C, (2010) A high-accuracy protein structural class prediction algorithm using predicted secondary structural information. J Theor Biol 267: 272-275.
    • (2010) J Theor Biol , vol.267 , pp. 272-275
    • Liu, T.1    Jia, C.2
  • 24
    • 76649141763 scopus 로고    scopus 로고
    • Prediction of protein structural classes for low-homology sequences based on predicted secondary structure
    • Yang JY, Peng ZL, Chen X, (2010) Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. BMC Bioinformatics 11: S9.
    • (2010) BMC Bioinformatics , vol.11
    • Yang, J.Y.1    Peng, Z.L.2    Chen, X.3
  • 25
    • 62549159517 scopus 로고    scopus 로고
    • Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation
    • Yang JY, Peng ZL, Yu ZG, Zhang RJ, Anh V, et al. (2009) Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation. J Theor Biol 257: 618-626.
    • (2009) J Theor Biol , vol.257 , pp. 618-626
    • Yang, J.Y.1    Peng, Z.L.2    Yu, Z.G.3    Zhang, R.J.4    Anh, V.5
  • 28
    • 0034141493 scopus 로고    scopus 로고
    • How good is prediction of protein structural class by the component-coupled method?
    • Wang ZX, Yuan Z, (2000) How good is prediction of protein structural class by the component-coupled method? Proteins-Structure Function and Genetics 38: 165-175.
    • (2000) Proteins-Structure Function and Genetics , vol.38 , pp. 165-175
    • Wang, Z.X.1    Yuan, Z.2
  • 29
    • 0033809190 scopus 로고    scopus 로고
    • Prediction of protein structural classes by neural network
    • Cai Y, Zhou G, (2000) Prediction of protein structural classes by neural network. Biochimie 82: 783-785.
    • (2000) Biochimie , vol.82 , pp. 783-785
    • Cai, Y.1    Zhou, G.2
  • 30
    • 33747182577 scopus 로고    scopus 로고
    • Classifier ensembles for protein structural class prediction with varying homology
    • Kedarisetti KD, Kurgan L, Dick S, (2006) Classifier ensembles for protein structural class prediction with varying homology. Biochem Biophys Res Commun 348: 981-988.
    • (2006) Biochem Biophys Res Commun , vol.348 , pp. 981-988
    • Kedarisetti, K.D.1    Kurgan, L.2    Dick, S.3
  • 31
    • 34247094836 scopus 로고    scopus 로고
    • Prediction of protein structural class for the twilight zone sequences
    • Kurgan L, Chen K, (2007) Prediction of protein structural class for the twilight zone sequences. Biochem Biophys Res Commun 357(2): 453-460.
    • (2007) Biochem Biophys Res Commun , vol.357 , Issue.2 , pp. 453-460
    • Kurgan, L.1    Chen, K.2
  • 32
    • 2942601555 scopus 로고    scopus 로고
    • Support vector machines for predicting protein structural class
    • Cai YD, Liu XJ, Xu X, Zhou GP, (2001) Support vector machines for predicting protein structural class. BMC Bioinformatics 2: 3.
    • (2001) BMC Bioinformatics , vol.2 , pp. 3
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.3    Zhou, G.P.4
  • 33
    • 0037423777 scopus 로고    scopus 로고
    • Support vector machines for prediction of protein domain structural class
    • Cai YD, Liu XJ, Xu XB, Chou KC, (2003) Support vector machines for prediction of protein domain structural class. J Theor Biol 221: 115-120.
    • (2003) J Theor Biol , vol.221 , pp. 115-120
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 34
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB, (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 35
    • 0035874145 scopus 로고    scopus 로고
    • Multiple linear regression for protein secondary structure prediction
    • Pan XM, (2001) Multiple linear regression for protein secondary structure prediction. Proteins 43: 256-259.
    • (2001) Proteins , vol.43 , pp. 256-259
    • Pan, X.M.1
  • 36
    • 0029157083 scopus 로고
    • Prediction of protein structural classes
    • Chou KC, Zhang CT, (1995) Prediction of protein structural classes. Crit Rev Biochem Mol Biol 30: 275-349.
    • (1995) Crit Rev Biochem Mol Biol , vol.30 , pp. 275-349
    • Chou, K.C.1    Zhang, C.T.2
  • 37
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner SE, Koehl P, Levitt M, (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 28: 254-256.
    • (2000) Nucleic Acids Res , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 38
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 39
    • 33748415440 scopus 로고    scopus 로고
    • Prediction of structural classes for protein sequences and domains-impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy
    • Kurgan L, Homaeian L, (2006) Prediction of structural classes for protein sequences and domains-impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy. Pattern Recognition. 39 (12): 2323-2343.
    • (2006) Pattern Recognition , vol.39 , Issue.12 , pp. 2323-2343
    • Kurgan, L.1    Homaeian, L.2
  • 40
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 41
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2


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