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Volumn 6, Issue 5, 2011, Pages

Identification of antifreeze proteins and their functional residues by support vector machine and genetic algorithms based on n-peptide compositions

Author keywords

[No Author keywords available]

Indexed keywords

ANTIFREEZE PROTEIN; ICE; N PEPTIDE; PEPTIDE; UNCLASSIFIED DRUG; FISH PROTEIN; INSECT PROTEIN;

EID: 79957871406     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020445     Document Type: Article
Times cited : (31)

References (38)
  • 2
    • 0034691564 scopus 로고    scopus 로고
    • Structural biology. Adding to the antifreeze agenda
    • Knight CA, (2000) Structural biology. Adding to the antifreeze agenda. Nature 406: 249-251.
    • (2000) Nature , vol.406 , pp. 249-251
    • Knight, C.A.1
  • 3
    • 0036923208 scopus 로고    scopus 로고
    • Cloning of an antifreeze protein gene in carrot and influence on freeze tolerance of transgenic tobaccos
    • Fan Y, Liu B, Wang HB, Wang SQ, Wang JF, (2002) Cloning of an antifreeze protein gene in carrot and influence on freeze tolerance of transgenic tobaccos. Plant Cell Rep 21: 296-301.
    • (2002) Plant Cell Rep , vol.21 , pp. 296-301
    • Fan, Y.1    Liu, B.2    Wang, H.B.3    Wang, S.Q.4    Wang, J.F.5
  • 4
    • 0026811103 scopus 로고
    • The cryoprotective effect of antifreeze glycopeptides from antarctic fishes
    • Rubinsky B, Arav A, Devries AL, (1992) The cryoprotective effect of antifreeze glycopeptides from antarctic fishes. Cryobiology 29: 69-79.
    • (1992) Cryobiology , vol.29 , pp. 69-79
    • Rubinsky, B.1    Arav, A.2    Devries, A.L.3
  • 5
    • 0029510888 scopus 로고
    • Antifreeze proteins and their potential use in frozen foods
    • Griffith M, Ewart KV, (1995) Antifreeze proteins and their potential use in frozen foods. Biotechnol Adv 13: 375-402.
    • (1995) Biotechnol Adv , vol.13 , pp. 375-402
    • Griffith, M.1    Ewart, K.V.2
  • 6
    • 4344568284 scopus 로고    scopus 로고
    • Antifreeze proteins in overwintering plants: a tale of two activities
    • Griffith M, Yaish MW, (2004) Antifreeze proteins in overwintering plants: a tale of two activities. Trends Plant Sci 9: 399-405.
    • (2004) Trends Plant Sci , vol.9 , pp. 399-405
    • Griffith, M.1    Yaish, M.W.2
  • 7
    • 0036470053 scopus 로고    scopus 로고
    • Antifreeze proteins: an unusual receptor-ligand interaction
    • Jia Z, Davies PL, (2002) Antifreeze proteins: an unusual receptor-ligand interaction. Trends Biochem Sci 27: 101-106.
    • (2002) Trends Biochem Sci , vol.27 , pp. 101-106
    • Jia, Z.1    Davies, P.L.2
  • 8
    • 49949083546 scopus 로고    scopus 로고
    • Lateral transfer of a lectin-like antifreeze protein gene in fishes
    • Graham LA, Lougheed SC, Ewart KV, Davies PL, (2008) Lateral transfer of a lectin-like antifreeze protein gene in fishes. PLoS ONE 3: e2616.
    • (2008) PLoS ONE , vol.3
    • Graham, L.A.1    Lougheed, S.C.2    Ewart, K.V.3    Davies, P.L.4
  • 9
    • 33746106845 scopus 로고    scopus 로고
    • Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions
    • Doxey AC, Yaish MW, Griffith M, McConkey BJ, (2006) Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions. Nat Biotechnol 24: 852-855.
    • (2006) Nat Biotechnol , vol.24 , pp. 852-855
    • Doxey, A.C.1    Yaish, M.W.2    Griffith, M.3    McConkey, B.J.4
  • 10
    • 4344642832 scopus 로고    scopus 로고
    • Cold survival in freeze-intolerant insects: the structure and function of beta-helical antifreeze proteins
    • Graether SP, Sykes BD, (2004) Cold survival in freeze-intolerant insects: the structure and function of beta-helical antifreeze proteins. Eur J Biochem 271: 3285-3296.
    • (2004) Eur J Biochem , vol.271 , pp. 3285-3296
    • Graether, S.P.1    Sykes, B.D.2
  • 11
    • 0033568338 scopus 로고    scopus 로고
    • Type I 'antifreeze' proteins. Structure-activity studies and mechanisms of ice growth inhibition
    • Harding MM, Ward LG, Haymet AD, (1999) Type I 'antifreeze' proteins. Structure-activity studies and mechanisms of ice growth inhibition. Eur J Biochem 264: 653-665.
    • (1999) Eur J Biochem , vol.264 , pp. 653-665
    • Harding, M.M.1    Ward, L.G.2    Haymet, A.D.3
  • 12
    • 0033597140 scopus 로고    scopus 로고
    • Quantitative and qualitative analysis of type III antifreeze protein structure and function
    • Graether SP, DeLuca CI, Baardsnes J, Hill GA, Davies PL, et al. (1999) Quantitative and qualitative analysis of type III antifreeze protein structure and function. J Biol Chem 274: 11842-11847.
    • (1999) J Biol Chem , vol.274 , pp. 11842-11847
    • Graether, S.P.1    DeLuca, C.I.2    Baardsnes, J.3    Hill, G.A.4    Davies, P.L.5
  • 13
    • 0034691594 scopus 로고    scopus 로고
    • Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect
    • Graether SP, Kuiper MJ, Gagne SM, Walker VK, Jia Z, et al. (2000) Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect. Nature 406: 325-328.
    • (2000) Nature , vol.406 , pp. 325-328
    • Graether, S.P.1    Kuiper, M.J.2    Gagne, S.M.3    Walker, V.K.4    Jia, Z.5
  • 14
    • 0029856558 scopus 로고    scopus 로고
    • Structural basis for the binding of a globular antifreeze protein to ice
    • Jia Z, DeLuca CI, Chao H, Davies PL, (1996) Structural basis for the binding of a globular antifreeze protein to ice. Nature 384: 285-288.
    • (1996) Nature , vol.384 , pp. 285-288
    • Jia, Z.1    DeLuca, C.I.2    Chao, H.3    Davies, P.L.4
  • 15
    • 58149148303 scopus 로고    scopus 로고
    • Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations
    • Nutt DR, Smith JC, (2008) Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. J Am Chem Soc 130: 13066-13073.
    • (2008) J Am Chem Soc , vol.130 , pp. 13066-13073
    • Nutt, D.R.1    Smith, J.C.2
  • 16
    • 0036093824 scopus 로고    scopus 로고
    • Crystal structure of beta-helical antifreeze protein points to a general ice binding model
    • Leinala EK, Davies PL, Jia Z, (2002) Crystal structure of beta-helical antifreeze protein points to a general ice binding model. Structure 10: 619-627.
    • (2002) Structure , vol.10 , pp. 619-627
    • Leinala, E.K.1    Davies, P.L.2    Jia, Z.3
  • 17
    • 10844235653 scopus 로고    scopus 로고
    • Optimal docking area: a new method for predicting protein-protein interaction sites
    • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R, (2005) Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 58: 134-143.
    • (2005) Proteins , vol.58 , pp. 134-143
    • Fernandez-Recio, J.1    Totrov, M.2    Skorodumov, C.3    Abagyan, R.4
  • 18
    • 33947429601 scopus 로고    scopus 로고
    • Predicting disulfide connectivity patterns
    • Lu CH, Chen YC, Yu CS, Hwang JK, (2007) Predicting disulfide connectivity patterns. Proteins 67: 262-270.
    • (2007) Proteins , vol.67 , pp. 262-270
    • Lu, C.H.1    Chen, Y.C.2    Yu, C.S.3    Hwang, J.K.4
  • 19
    • 33746218840 scopus 로고    scopus 로고
    • Prediction of protein subcellular localization
    • Yu CS, Chen YC, Lu CH, Hwang JK, (2006) Prediction of protein subcellular localization. Proteins 64: 643-651.
    • (2006) Proteins , vol.64 , pp. 643-651
    • Yu, C.S.1    Chen, Y.C.2    Lu, C.H.3    Hwang, J.K.4
  • 20
    • 1942505330 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions
    • Yu CS, Lin CJ, Hwang JK, (2004) Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 13: 1402-1406.
    • (2004) Protein Sci , vol.13 , pp. 1402-1406
    • Yu, C.S.1    Lin, C.J.2    Hwang, J.K.3
  • 21
    • 0037341893 scopus 로고    scopus 로고
    • Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets
    • Yu CS, Wang JY, Yang JM, Lyu PC, Lin CJ, et al. (2003) Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets. Proteins 50: 531-536.
    • (2003) Proteins , vol.50 , pp. 531-536
    • Yu, C.S.1    Wang, J.Y.2    Yang, J.M.3    Lyu, P.C.4    Lin, C.J.5
  • 22
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G, Dunbrack RL Jr, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 25
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch A, Apweiler R, (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28: 45-48.
    • (2000) Nucleic Acids Res , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 26
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38: D142-148.
    • Nucleic Acids Res , vol.38
  • 27
    • 33646153778 scopus 로고    scopus 로고
    • Solution structure of the antifreeze-like domain of human sialic acid synthase
    • Hamada T, Ito Y, Abe T, Hayashi F, Guntert P, et al. (2006) Solution structure of the antifreeze-like domain of human sialic acid synthase. Protein Sci 15: 1010-1016.
    • (2006) Protein Sci , vol.15 , pp. 1010-1016
    • Hamada, T.1    Ito, Y.2    Abe, T.3    Hayashi, F.4    Guntert, P.5
  • 28
    • 27544440502 scopus 로고    scopus 로고
    • Prediction of disulfide connectivity from protein sequences
    • Chen YC, Hwang JK, (2005) Prediction of disulfide connectivity from protein sequences. Proteins 61: 507-512.
    • (2005) Proteins , vol.61 , pp. 507-512
    • Chen, Y.C.1    Hwang, J.K.2
  • 29
    • 0033151954 scopus 로고    scopus 로고
    • Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification
    • Dubchak I, Muchnik I, Mayor C, Dralyuk I, Kim SH, (1999) Recognition of a protein fold in the context of the Structural Classification of Proteins (SCOP) classification. Proteins 35: 401-407.
    • (1999) Proteins , vol.35 , pp. 401-407
    • Dubchak, I.1    Muchnik, I.2    Mayor, C.3    Dralyuk, I.4    Kim, S.H.5
  • 30
    • 79957800580 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines. Software available from
    • Chang CC, Lin CJ, (2001) LIBSVM: a library for support vector machines. Software available fromhttp://www.csie.ntu.edu.tw/~cjlin/libsvm.
    • (2001)
    • Chang, C.C.1    Lin, C.J.2
  • 32
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW, (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 33
    • 0023984847 scopus 로고
    • Optimal alignments in linear space
    • Myers EW, Miller W, (1988) Optimal alignments in linear space. Comput Appl Biosci 4: 11-17.
    • (1988) Comput Appl Biosci , vol.4 , pp. 11-17
    • Myers, E.W.1    Miller, W.2
  • 34
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B, (1999) Twilight zone of protein sequence alignments. Protein Eng 12: 85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 35
    • 0029013417 scopus 로고
    • Ice-binding structure and mechanism of an antifreeze protein from winter flounder
    • Sicheri F, Yang DS, (1995) Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature 375: 427-431.
    • (1995) Nature , vol.375 , pp. 427-431
    • Sicheri, F.1    Yang, D.S.2
  • 36
    • 0034691568 scopus 로고    scopus 로고
    • Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein
    • Liou YC, Tocilj A, Davies PL, Jia Z, (2000) Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein. Nature 406: 322-324.
    • (2000) Nature , vol.406 , pp. 322-324
    • Liou, Y.C.1    Tocilj, A.2    Davies, P.L.3    Jia, Z.4
  • 37
    • 0003845223 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System
    • In: Scientific D, editors, San Carlos, CA, USA
    • DeLano WL, (2002) The PyMOL Molecular Graphics System In: Scientific D, editors. San Carlos, CA, USA. http://www.pymol.org.
    • (2002)
    • DeLano, W.L.1
  • 38
    • 48249101260 scopus 로고    scopus 로고
    • X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers
    • Pentelute BL, Gates ZP, Tereshko V, Dashnau JL, Vanderkooi JM, et al. (2008) X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers. J Am Chem Soc 130: 9695-9701.
    • (2008) J Am Chem Soc , vol.130 , pp. 9695-9701
    • Pentelute, B.L.1    Gates, Z.P.2    Tereshko, V.3    Dashnau, J.L.4    Vanderkooi, J.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.