메뉴 건너뛰기




Volumn 267, Issue 3, 2010, Pages 312-318

Predicting the state of cysteines based on sequence information

Author keywords

Annotation information; Evolution information; F score function.; Support vector machine

Indexed keywords

CYSTEINE;

EID: 77956673246     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.09.002     Document Type: Article
Times cited : (6)

References (42)
  • 1
    • 0141990705 scopus 로고    scopus 로고
    • Predicting the disulfide bonding state of cysteines with combinations of kernel machines
    • Ceroni A., Frasconi P., Passerini A., Vullo A. Predicting the disulfide bonding state of cysteines with combinations of kernel machines. J. VLSI. Signal Process. Syst. 2003, 35:287-295.
    • (2003) J. VLSI. Signal Process. Syst. , vol.35 , pp. 287-295
    • Ceroni, A.1    Frasconi, P.2    Passerini, A.3    Vullo, A.4
  • 2
    • 2542586190 scopus 로고    scopus 로고
    • Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences
    • Chen Y.C., Lin S.C., Lin C.J., Hwang J.K. Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. Proteins 2004, 55:1036-1042.
    • (2004) Proteins , vol.55 , pp. 1036-1042
    • Chen, Y.C.1    Lin, S.C.2    Lin, C.J.3    Hwang, J.K.4
  • 4
    • 57649181721 scopus 로고    scopus 로고
    • Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
    • Cheng C.W., Su E.C.Y., Hwang J.K., Sung T.Y., Hsu W.L. Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics 2008, 9:S6.
    • (2008) BMC Bioinformatics , vol.9
    • Cheng, C.W.1    Su, E.C.Y.2    Hwang, J.K.3    Sung, T.Y.4    Hsu, W.L.5
  • 5
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo-amino acid composition
    • Chou K.C. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 2001, 43:246-255.
    • (2001) Proteins , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 6
    • 0037195776 scopus 로고    scopus 로고
    • Using functional domain composition and support vector machines for prediction of protein subcellular location
    • Chou K.C., Cai Y.D. Using functional domain composition and support vector machines for prediction of protein subcellular location. J. Biol. Chem. 2002, 277:45765-45769.
    • (2002) J. Biol. Chem. , vol.277 , pp. 45765-45769
    • Chou, K.C.1    Cai, Y.D.2
  • 7
    • 33748944288 scopus 로고    scopus 로고
    • Predicting protein subcellular location by fusing multiple classifiers
    • Chou K.C., Shen H.B. Predicting protein subcellular location by fusing multiple classifiers. J. Cell. Biochem. 2006, 99:517-527.
    • (2006) J. Cell. Biochem. , vol.99 , pp. 517-527
    • Chou, K.C.1    Shen, H.B.2
  • 8
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou K.C., Shen H.B. Recent progress in protein subcellular location prediction. Anal. Biochem. 2007, 370:1-16.
    • (2007) Anal. Biochem. , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 9
    • 77958152094 scopus 로고
    • Proteins: Structures and Molecular Properties, New York.
    • Creighton, T., 1993. Proteins: Structures and Molecular Properties, New York.
    • (1993)
    • Creighton, T.1
  • 11
    • 29144499905 scopus 로고    scopus 로고
    • Working set selection using order information for training SVM
    • Fan R.E., Chen P.H., Lin C.J. Working set selection using order information for training SVM. J. Mach. Learn. Res. 2005, 6:1889-1918.
    • (2005) J. Mach. Learn. Res. , vol.6 , pp. 1889-1918
    • Fan, R.E.1    Chen, P.H.2    Lin, C.J.3
  • 13
    • 0033566578 scopus 로고    scopus 로고
    • Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins
    • Fariselli P., Riccobelli P., Casadio R. Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. Proteins 1999, 36:340-346.
    • (1999) Proteins , vol.36 , pp. 340-346
    • Fariselli, P.1    Riccobelli, P.2    Casadio, R.3
  • 14
    • 19544393195 scopus 로고    scopus 로고
    • Disulfide connectivity prediction using secondary structure information and diresidue frequencies
    • Ferre F., Clote P. Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics 2005, 21:2336-2346.
    • (2005) Bioinformatics , vol.21 , pp. 2336-2346
    • Ferre, F.1    Clote, P.2
  • 15
    • 23144437891 scopus 로고    scopus 로고
    • DiANNA: a web server for disulfide connectivity prediction
    • Ferre F., Clote P. DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res. 2005, 33:W230-W232.
    • (2005) Nucleic Acids Res. , vol.33
    • Ferre, F.1    Clote, P.2
  • 16
    • 0034039497 scopus 로고    scopus 로고
    • Predicting the oxidation state of cysteines by multiple sequence alignment
    • Fiser A., Simon I. Predicting the oxidation state of cysteines by multiple sequence alignment. Bioinformatics 2000, 16:251-256.
    • (2000) Bioinformatics , vol.16 , pp. 251-256
    • Fiser, A.1    Simon, I.2
  • 17
    • 0026579140 scopus 로고
    • Different sequence environments of cysteines and half cystines in proteins application to predict disulfide forming residues
    • Fiser A., Cserzo M., Tudos E., Simon I. Different sequence environments of cysteines and half cystines in proteins application to predict disulfide forming residues. FEBS Lett. 1992, 302:117-120.
    • (1992) FEBS Lett. , vol.302 , pp. 117-120
    • Fiser, A.1    Cserzo, M.2    Tudos, E.3    Simon, I.4
  • 18
    • 44349159560 scopus 로고    scopus 로고
    • Using support vector machine combined with auto covariance to predict proteinprotein interactions from protein sequences
    • Guo Y.Z., Yu L.Z., Wen Z.N., Li M.L. Using support vector machine combined with auto covariance to predict proteinprotein interactions from protein sequences. Nucleic Acids Res. 2008, 36:3025-3030.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3025-3030
    • Guo, Y.Z.1    Yu, L.Z.2    Wen, Z.N.3    Li, M.L.4
  • 19
    • 33748254329 scopus 로고    scopus 로고
    • Predicting G-protein coupled receptors-G-protein coupling specificity based on autocross-covariance transform
    • Guo Y.Z., Li M.L., Lu M.C., Wen Z.N., Huang Z.T. Predicting G-protein coupled receptors-G-protein coupling specificity based on autocross-covariance transform. Proteins 2006, 65:55-60.
    • (2006) Proteins , vol.65 , pp. 55-60
    • Guo, Y.Z.1    Li, M.L.2    Lu, M.C.3    Wen, Z.N.4    Huang, Z.T.5
  • 20
    • 33745102264 scopus 로고    scopus 로고
    • Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform
    • Guo Y.Z., Li M., Lu M., Wen Z., Wang K., Li G., Wu J. Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform. Amino Acids 2006, 30:397-402.
    • (2006) Amino Acids , vol.30 , pp. 397-402
    • Guo, Y.Z.1    Li, M.2    Lu, M.3    Wen, Z.4    Wang, K.5    Li, G.6    Wu, J.7
  • 21
    • 0037397499 scopus 로고    scopus 로고
    • Disulfide bonds as switches for protein function
    • Hogg P.J. Disulfide bonds as switches for protein function. Trends Biochem. Sci. 2003, 28:210-214.
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 210-214
    • Hogg, P.J.1
  • 22
    • 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. 1999, 292:195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 23
    • 0036937367 scopus 로고    scopus 로고
    • Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks
    • Martelli P.L., Fariselli P., Malaguti L., Casadio R. Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng. 2002, 15:951-953.
    • (2002) Protein Eng. , vol.15 , pp. 951-953
    • Martelli, P.L.1    Fariselli, P.2    Malaguti, L.3    Casadio, R.4
  • 24
    • 0036839271 scopus 로고    scopus 로고
    • Prediction of the disuffide-bonding state of cysteines in proteins at 88% accuracy
    • Martelli P.L., Fariselli P., Malaguti L., Casadio R. Prediction of the disuffide-bonding state of cysteines in proteins at 88% accuracy. Protein Sci. 2003, 11:2735-2739.
    • (2003) Protein Sci. , vol.11 , pp. 2735-2739
    • Martelli, P.L.1    Fariselli, P.2    Malaguti, L.3    Casadio, R.4
  • 25
    • 0016772212 scopus 로고
    • Comparison of predicted and observed secondary structure of T4 phage lysozyme
    • Matthews B.W. Comparison of predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta. 1975, 405:442-451.
    • (1975) Biochim. Biophys. Acta. , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 26
    • 0037083493 scopus 로고    scopus 로고
    • Predicting the disulfide bonding state of cysteines using protein descriptors
    • Mucchielli-Giorgi M.H.M., Hazout S., Tuffery P. Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins 2002, 46:243-249.
    • (2002) Proteins , vol.46 , pp. 243-249
    • Mucchielli-Giorgi, M.H.M.1    Hazout, S.2    Tuffery, P.3
  • 27
    • 0025118064 scopus 로고
    • Prediction of the disulfide-bonding state of cysteine in proteins
    • Muskal S.M., Holbrook S.R., Kim S.H. Prediction of the disulfide-bonding state of cysteine in proteins. Protein Eng. 1990, 3:667-672.
    • (1990) Protein Eng. , vol.3 , pp. 667-672
    • Muskal, S.M.1    Holbrook, S.R.2    Kim, S.H.3
  • 28
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
    • Radzicka A., Wolfenden R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 1988, 27:1664-1670.
    • (1988) Biochemistry , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 30
    • 36448952353 scopus 로고    scopus 로고
    • Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM
    • Shen H.B., Chou K.C. Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Eng. Des. Sel. 2007, 20:561-567.
    • (2007) Protein Eng. Des. Sel. , vol.20 , pp. 561-567
    • Shen, H.B.1    Chou, K.C.2
  • 31
    • 33847637338 scopus 로고    scopus 로고
    • Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction
    • Shen H.B., Yang J., Chou K.C. Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction. Amino Acids 2007, 33:57-67.
    • (2007) Amino Acids , vol.33 , pp. 57-67
    • Shen, H.B.1    Yang, J.2    Chou, K.C.3
  • 32
    • 4444249440 scopus 로고    scopus 로고
    • Cooperativity of the oxidization of cysteines in globular proteins
    • Song J.N., Li W.J., Xu W.B. Cooperativity of the oxidization of cysteines in globular proteins. J. Theor. Biol. 2004, 231:85-95.
    • (2004) J. Theor. Biol. , vol.231 , pp. 85-95
    • Song, J.N.1    Li, W.J.2    Xu, W.B.3
  • 33
    • 1942456707 scopus 로고    scopus 로고
    • Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition
    • Song J.N., Wang M.L., Li W.J., Xu W.B. Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition. Biochem. Biophys. Res. Commun. 2004, 318:142-147.
    • (2004) Biochem. Biophys. Res. Commun. , vol.318 , pp. 142-147
    • Song, J.N.1    Wang, M.L.2    Li, W.J.3    Xu, W.B.4
  • 34
    • 36549021546 scopus 로고    scopus 로고
    • Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
    • Song J.N., Yuan Z., Tan H., Huber T., Burrage K. Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinformatics 2007, 23:3147-3154.
    • (2007) Bioinformatics , vol.23 , pp. 3147-3154
    • Song, J.N.1    Yuan, Z.2    Tan, H.3    Huber, T.4    Burrage, K.5
  • 35
    • 8844261124 scopus 로고    scopus 로고
    • Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor
    • Tessier D., Bardiaux B., Larre C., Popineau Y. Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor. Bioinformatics 2004, 20:2509-2512.
    • (2004) Bioinformatics , vol.20 , pp. 2509-2512
    • Tessier, D.1    Bardiaux, B.2    Larre, C.3    Popineau, Y.4
  • 37
    • 0035098779 scopus 로고    scopus 로고
    • Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability
    • Vieille C., Zeikus G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 2001, 65:1-43.
    • (2001) Microbiol. Mol. Biol. Rev. , vol.65 , pp. 1-43
    • Vieille, C.1    Zeikus, G.J.2
  • 38
    • 0029738872 scopus 로고    scopus 로고
    • Experimentally determined hydrophobicity scale for proteins at membrane interfaces
    • Wimley W.C., White S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 1996, 3:842-848.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 842-848
    • Wimley, W.C.1    White, S.H.2
  • 39
    • 0028943316 scopus 로고
    • Disulfide bond formation and eukaryotic secretory productivity
    • Wittrup K.D. Disulfide bond formation and eukaryotic secretory productivity. Curr. Opin. Biotechnol. 1995, 6:203-208.
    • (1995) Curr. Opin. Biotechnol. , vol.6 , pp. 203-208
    • Wittrup, K.D.1
  • 40
    • 77958150544 scopus 로고    scopus 로고
    • Using position specific scoring matrix and auto covariance to predict protein subnuclear localization
    • Xiao R.Q., Guo Y.Z., Zeng Y.H., Tan H.F., Pu X.M., Li M.L. Using position specific scoring matrix and auto covariance to predict protein subnuclear localization. J. Biomed. Sci. Eng. 2009, 2:51-56.
    • (2009) J. Biomed. Sci. Eng. , vol.2 , pp. 51-56
    • Xiao, R.Q.1    Guo, Y.Z.2    Zeng, Y.H.3    Tan, H.F.4    Pu, X.M.5    Li, M.L.6
  • 41
    • 67349244013 scopus 로고    scopus 로고
    • Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach
    • Zeng Y.H., Guo Y.Z., Xiao R.Q., Yang L., Yu L.Z., Li M.L. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J. Theor. Biol. 2009, 259:366-372.
    • (2009) J. Theor. Biol. , vol.259 , pp. 366-372
    • Zeng, Y.H.1    Guo, Y.Z.2    Xiao, R.Q.3    Yang, L.4    Yu, L.Z.5    Li, M.L.6
  • 42
    • 49749132014 scopus 로고    scopus 로고
    • Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine
    • Zhou X.B., Chen C., Li Z.C., Zou X.Y. Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine. Amino Acids 2008, 35:383-388.
    • (2008) Amino Acids , vol.35 , pp. 383-388
    • Zhou, X.B.1    Chen, C.2    Li, Z.C.3    Zou, X.Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.