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Volumn 4774 LNBI, Issue , 2007, Pages 108-119

SVM-BetaPred: Prediction of right-handed ß-helix fold from protein sequence Using SVM

Author keywords

Fold recognition; Pectate lyase; PSSM; Secondary structure; helix fold; sheet stacking; Support vector machines; SVM

Indexed keywords

ANTIBIOTICS; DATA STRUCTURES; HEALTH RISKS; SUPPORT VECTOR MACHINES;

EID: 38349104051     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-75286-8_11     Document Type: Conference Paper
Times cited : (1)

References (29)
  • 1
    • 0035910068 scopus 로고    scopus 로고
    • BETAWRAP: Successful prediction of parallel beta helices from primary sequence reveals an association with many microbial pathogens
    • Bradley, P., Cowen, L., Menke, M., King, J., Berger, B.: BETAWRAP: Successful prediction of parallel beta helices from primary sequence reveals an association with many microbial pathogens. Proc. Natl. Acad. Sci. 98, 14819-14824 (2001)
    • (2001) Proc. Natl. Acad. Sci , vol.98 , pp. 14819-14824
    • Bradley, P.1    Cowen, L.2    Menke, M.3    King, J.4    Berger, B.5
  • 2
    • 0029257535 scopus 로고    scopus 로고
    • The parallel ßhelix and other coiled folds
    • Yoder, M.D., Jurnak, F.: The parallel ßhelix and other coiled folds. FASEB J. 9(5), 335-342 (1999)
    • (1999) FASEB J , vol.9 , Issue.5 , pp. 335-342
    • Yoder, M.D.1    Jurnak, F.2
  • 4
    • 0027329090 scopus 로고
    • New domain motif: The structure of pectate lyase C., a secreted plant virulence factor
    • Yonder, M., Keen, N., Jurnak, F.: New domain motif: The structure of pectate lyase C., a secreted plant virulence factor. Science 260(5113), 1503-1507 (1993)
    • (1993) Science , vol.260 , Issue.5113 , pp. 1503-1507
    • Yonder, M.1    Keen, N.2    Jurnak, F.3
  • 6
    • 33644841706 scopus 로고    scopus 로고
    • Conformational and Sequence Signatures in ß Helix Proteins
    • Iengar, P., Joshi, N.V., Padmanabhan, B.: Conformational and Sequence Signatures in ß Helix Proteins. Structure 14(3), 529-542 (2006)
    • (2006) Structure , vol.14 , Issue.3 , pp. 529-542
    • Iengar, P.1    Joshi, N.V.2    Padmanabhan, B.3
  • 7
    • 0034492510 scopus 로고    scopus 로고
    • ßeta-helix core packing within the triple-stranded oligomerization domain of P22 tailspike
    • Kreisberg, J.F., Betts, S.D., King, J.: ßeta-helix core packing within the triple-stranded oligomerization domain of P22 tailspike. Protein Sci. 9(12), 2338-2343 (2000)
    • (2000) Protein Sci , vol.9 , Issue.12 , pp. 2338-2343
    • Kreisberg, J.F.1    Betts, S.D.2    King, J.3
  • 8
    • 0031688287 scopus 로고    scopus 로고
    • Jenkins, J., Mayans, O., Pickersgill, R.: Structure and evolution of parallel helix proteins. Journal of Struct. Biol. 122, 236-246 (1998)
    • Jenkins, J., Mayans, O., Pickersgill, R.: Structure and evolution of parallel helix proteins. Journal of Struct. Biol. 122, 236-246 (1998)
  • 9
    • 0036358995 scopus 로고    scopus 로고
    • The spectrum kernel: A string kernel for SVM protein classification
    • Leslie, C., Eskin, E., Noble, W.S.: The spectrum kernel: a string kernel for SVM protein classification. Pac. Symp. Biocomput., 564-575 (2002)
    • (2002) Pac. Symp. Biocomput , vol.564-575
    • Leslie, C.1    Eskin, E.2    Noble, W.S.3
  • 10
    • 33745616114 scopus 로고    scopus 로고
    • A machine learning information retrieval approach to protein fold recognition
    • Cheng, J., Baldi, P.: A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22(12), 1456-1463 (2006)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1456-1463
    • Cheng, J.1    Baldi, P.2
  • 11
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for investigation of sequences and structures
    • Murzin, A., Brenner, S., Hubbard, T., Chothia, C.: SCOP: a structural classification of proteins database for investigation of sequences and structures. J. Mol. Bio. 297, 536-540 (1995)
    • (1995) J. Mol. Bio , vol.297 , pp. 536-540
    • Murzin, A.1    Brenner, S.2    Hubbard, T.3    Chothia, C.4
  • 13
    • 0029259085 scopus 로고
    • Maximum discrimination hidden Markov models of sequence consensus
    • Eddy, S., Mitchison, G., Durbin, R.: Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol. 2, 9-23 (1995)
    • (1995) J. Comput. Biol , vol.2 , pp. 9-23
    • Eddy, S.1    Mitchison, G.2    Durbin, R.3
  • 15
    • 0033957834 scopus 로고    scopus 로고
    • Apweiler: The SWISS-PROT protein daabse and its supplement TrEMBL in 2000
    • Bairoch, A., Apweiler: The SWISS-PROT protein daabse and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48 (2000)
    • (2000) Nucleic Acids Res , vol.28 , pp. 45-48
    • Bairoch, A.1
  • 16
    • 2942616602 scopus 로고    scopus 로고
    • Evidence for assembly of prions with left-handed beta-helices into trimers
    • Govaerts, C., Wille, H., Prusiner, S.B., Cohen, F.E.: Evidence for assembly of prions with left-handed beta-helices into trimers. Proc. Natl. Acad. Sci. USA 101(22), 8342-8347 (2004)
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.22 , pp. 8342-8347
    • Govaerts, C.1    Wille, H.2    Prusiner, S.B.3    Cohen, F.E.4
  • 17
    • 0036699189 scopus 로고    scopus 로고
    • Sequence clustering strategies improve remote homology recognitions while reducing search times
    • Li, W., Jaroszewski, L., Godzik, A.: Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 15(8), 643-649 (2002)
    • (2002) Protein Eng , vol.15 , Issue.8 , pp. 643-649
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 18
    • 0036086337 scopus 로고    scopus 로고
    • Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions
    • Zavaljevski, N., Stevens, F.J., Reifman, J.: Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions. Bioinformatics 18, 689-696 (2002)
    • (2002) Bioinformatics , vol.18 , pp. 689-696
    • Zavaljevski, N.1    Stevens, F.J.2    Reifman, J.3
  • 19
    • 3242877807 scopus 로고    scopus 로고
    • ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
    • Bhasin, M., Raghava, G.P.S.: ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Research 32, W414-W419 (2004)
    • (2004) Nucleic Acids Research , vol.32
    • Bhasin, M.1    Raghava, G.P.S.2
  • 21
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale SVM learning practical
    • Scholkopf, B, Burges, C, Smola, A, eds, MIT Press, Cambridge, MA, London, England
    • Joachims, T.: Making large-scale SVM learning practical. In: Scholkopf, B., Burges, C., Smola, A. (eds.) Advances in Kernel Methods-Support Vector Learning. MIT Press, Cambridge, MA, London, England (1999)
    • (1999) Advances in Kernel Methods-Support Vector Learning
    • Joachims, T.1
  • 22
    • 33646195908 scopus 로고    scopus 로고
    • Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
    • Song, J., Burrage, K., Yuan, Z., Huber, T.: Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information. BMC Bioinformatics 7, 124 (2006)
    • (2006) BMC Bioinformatics , vol.7 , pp. 124
    • Song, J.1    Burrage, K.2    Yuan, Z.3    Huber, T.4
  • 23
    • 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. 405, 442-451 (1975)
    • (1975) Biochim. Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 24
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice, P., Longden, I., Bleasby, A.: EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16(6), 276-277 (2000)
    • (2000) Trends in Genetics , vol.16 , Issue.6 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 25
    • 3343003521 scopus 로고    scopus 로고
    • Hepatitis C virus whole genome position weight matrix and robust primer design
    • Qiu, P., Cai, X.Y., Wang, L., Greene, J., Malcolm, B.: Hepatitis C virus whole genome position weight matrix and robust primer design. BMC Microbiology 2,29 (2002)
    • (2002) BMC Microbiology , vol.2 , pp. 29
    • Qiu, P.1    Cai, X.Y.2    Wang, L.3    Greene, J.4    Malcolm, B.5
  • 27
    • 0037449787 scopus 로고    scopus 로고
    • The Tailspike Protein of Shigella Phage Sf6
    • Freiberg, A., Morona, R., Bosch, L., Baxa, U.: The Tailspike Protein of Shigella Phage Sf6. J. Biol. Chem. 278(3), 1542-1548 (2003)
    • (2003) J. Biol. Chem , vol.278 , Issue.3 , pp. 1542-1548
    • Freiberg, A.1    Morona, R.2    Bosch, L.3    Baxa, U.4
  • 28
    • 85156241986 scopus 로고    scopus 로고
    • Prediction of b sheets in protein
    • Touretzky, D.S, Mozer, M.C, Hasaselmo, M.E, eds, MIT Press, Cambridge, MA
    • Krogh, A., Riis, S.K.: Prediction of b sheets in protein. In: Touretzky, D.S., Mozer, M.C., Hasaselmo, M.E. (eds.) Advances in Neural Information Processing System 8, pp. 917-923. MIT Press, Cambridge, MA (1996)
    • (1996) Advances in Neural Information Processing System , vol.8 , pp. 917-923
    • Krogh, A.1    Riis, S.K.2
  • 29
    • 0027997161 scopus 로고
    • The DEF database of sequence based protein fold class prediction
    • Reczko, M., Bohr, H.: The DEF database of sequence based protein fold class prediction. Nucleic Acid Res. 22, 3616-3619 (1995)
    • (1995) Nucleic Acid Res , vol.22 , pp. 3616-3619
    • Reczko, M.1    Bohr, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.