메뉴 건너뛰기




Volumn 14, Issue 5, 2005, Pages 849-865

Prediction of contact maps using Support Vector Machines

Author keywords

Contact map prediction; Correlated mutation analysis; Support vector machines

Indexed keywords


EID: 33746208821     PISSN: 02182130     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218213005002429     Document Type: Article
Times cited : (5)

References (32)
  • 1
    • 0034635337 scopus 로고    scopus 로고
    • Exploring local and non-local interactions for protein stability by structural motif engineering
    • M. Niggemann and B. Steipe, Exploring local and non-local interactions for protein stability by structural motif engineering. J. Mol. Biol., 296:181-195, 2000.
    • (2000) J. Mol. Biol. , vol.296 , pp. 181-195
    • Niggemann, M.1    Steipe, B.2
  • 2
    • 0029155772 scopus 로고
    • Impact of local and non-local interactions on thermodynamics and kinetics of protein folding
    • V. I. Abkevich, A. M. Gutin, and E. I. Shakhnovich, Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol., 252:460-471, 1995.
    • (1995) J. Mol. Biol. , vol.252 , pp. 460-471
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 3
    • 0030777760 scopus 로고    scopus 로고
    • Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
    • D. Gilis and M. Rooman, Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J. Mol. Biol., 272:276-290, 1997.
    • (1997) J. Mol. Biol. , vol.272 , pp. 276-290
    • Gilis, D.1    Rooman, M.2
  • 4
    • 0026511656 scopus 로고
    • The folding of an enzyme, I. Theory of protein engineering analysis of stability and pathways of protein folding
    • A. R. Fersht, A. Matouschek and L. Serrano, The folding of an enzyme, i. theory of protein engineering analysis of stability and pathways of protein folding. J. Mol. Biol., 224:771-782, 1992.
    • (1992) J. Mol. Biol. , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 5
    • 0002682169 scopus 로고    scopus 로고
    • Local versus nonlocal interactions in protein folding and stability-an experimentalist's point of view
    • V. Muñoz and L. Serrano, Local versus nonlocal interactions in protein folding and stability-an experimentalist's point of view. Folding & Design, 1:R71-77, 1996.
    • (1996) Folding & Design , vol.1
    • Muñoz, V.1    Serrano, L.2
  • 6
    • 0026553768 scopus 로고
    • The folding of an enzyme, II. Substructure of barnase and the contribution of different interactions to protein stability
    • L. Serrano, J. T. Kellis, Jr., P. Cann, A. Matouschek and A. R. Fersht, The folding of an enzyme, ii. substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol., 224:783-804, 1992.
    • (1992) J. Mol. Biol. , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis Jr., J.T.2    Cann, P.3    Matouschek, A.4    Fersht, A.R.5
  • 7
    • 0024295240 scopus 로고
    • Contribution of hydrophobic interactions to protein stability
    • J. T. Kellis, Jr., K. Nyberg, D. Sali and A. R. Fersht, Contribution of hydrophobic interactions to protein stability. Nature, 333:784-786, 1988.
    • (1988) Nature , vol.333 , pp. 784-786
    • Kellis Jr., J.T.1    Nyberg, K.2    Sali, D.3    Fersht, A.R.4
  • 8
    • 0025787845 scopus 로고
    • Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the Ile-96 - Ala mutation in barnase
    • M. Prevost, S. J. Wodak, B. Tidor and M. Karplus, Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96 - ala mutation in barnase. Proc. Natl. Acad. Sci., 88:10880-10884, 1991.
    • (1991) Proc. Natl. Acad. Sci. , vol.88 , pp. 10880-10884
    • Prevost, M.1    Wodak, S.J.2    Tidor, B.3    Karplus, M.4
  • 9
    • 0030627407 scopus 로고    scopus 로고
    • Recovery of protein structure from contact maps
    • M. Vendruscolo, E. Russell and E. Domany, Recovery of protein structure from contact maps. Folding & Design, 2:295-306, 1997.
    • (1997) Folding & Design , vol.2 , pp. 295-306
    • Vendruscolo, M.1    Russell, E.2    Domany, E.3
  • 10
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • P. Fariselli, Osvaldo Olmea, Alfonso Valencia and Rita Casadio, Prediction of contact maps with neural networks and correlated mutations. Protein Eng., 14(11):835-843, 2001.
    • (2001) Protein Eng. , vol.14 , Issue.11 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 11
    • 0033550256 scopus 로고    scopus 로고
    • Effective use of sequence correlation and conservation in fold recognition
    • O. Olmea, Burkhard Rost and Alfonso Valencia, Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol., 293:1221-1239, 1999.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1221-1239
    • Olmea, O.1    Rost, B.2    Valencia, A.3
  • 12
    • 0029850738 scopus 로고    scopus 로고
    • The prediction of protein contacts from multiple sequence alignments
    • D. Thomas, G. Casari and C Sander, The prediction of protein contacts from multiple sequence alignments. Protein Engineering, 9(11):941-948, 1996.
    • (1996) Protein Engineering , vol.9 , Issue.11 , pp. 941-948
    • Thomas, D.1    Casari, G.2    Sander, C.3
  • 14
    • 0041719954 scopus 로고    scopus 로고
    • Prediction of contact maps by recurrent neural network architectures and hidden context propagation from all four cardinal corners
    • G. Pollastri and P. Baldi, Prediction of contact maps by recurrent neural network architectures and hidden context propagation from all four cardinal corners. Bioinformatics, 18 Suppl 1:S62-S70, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.1 SUPPL.
    • Pollastri, G.1    Baldi, P.2
  • 15
    • 0033648770 scopus 로고    scopus 로고
    • Recognition of protein structure: Determining the relative energetic contributions of beta-strands, alpha-helices and loops
    • B. Reva and S. Topiol, Recognition of protein structure: Determining the relative energetic contributions of beta-strands, alpha-helices and loops. In Proc. of The Pacific Symposium on Biocomputing, pages 165-175, 2000.
    • (2000) Proc. of the Pacific Symposium on Biocomputing , pp. 165-175
    • Reva, B.1    Topiol, S.2
  • 18
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • A. G. Murzin, S. E. Brenner, T. Hubbard and C. Chothia, SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247:536-540, 1995.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 23
    • 0035957531 scopus 로고    scopus 로고
    • A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach
    • S. Hua and Sun Z, A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach. J. Mol. Biol., 308:397-407, 2001.
    • (2001) J. Mol. Biol. , vol.308 , pp. 397-407
    • Hua, S.1    Sun, Z.2
  • 24
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • D. D. Pollock and W. R. Taylor, Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Engineering, 10:647-657, 1997.
    • (1997) Protein Engineering , vol.10 , pp. 647-657
    • Pollock, D.D.1    Taylor, W.R.2
  • 25
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • D. D. Pollock, W. R. Taylor and N. Goldman, Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol., 287:187-198, 1999.
    • (1999) J. Mol. Biol. , vol.287 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 26
    • 0034794239 scopus 로고    scopus 로고
    • Evaluation of a novel method for the identification of coevolving protein residues
    • P. Pritchard, Peter Bladon, Jane M. O. Mitchell and Mark J. Dufton, Evaluation of a novel method for the identification of coevolving protein residues. Protein Eng., 14(8):549-555, 2001.
    • (2001) Protein Eng. , vol.14 , Issue.8 , pp. 549-555
    • Pritchard, P.1    Bladon, P.2    Mitchell, J.M.O.3    Dufton, M.J.4
  • 27
    • 0015243774 scopus 로고
    • Test for comparing related aminoacid sequences
    • A. D. McLachlan, Test for comparing related aminoacid sequences. J. Mol. Biol., 61:409-424, 1971.
    • (1971) J. Mol. Biol. , vol.61 , pp. 409-424
    • McLachlan, A.D.1
  • 28
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale svm learning practical
    • B. Schlkopf and C. Burges and A. Smola (ed.), MIT-Press, 1999
    • T. Joachims, Making large-scale svm learning practical. Advances in Kernel Methods - Support Vector Learning, B. Schlkopf and C. Burges and A. Smola (ed.), MIT-Press, 1999, 1999.
    • (1999) Advances in Kernel Methods - Support Vector Learning
    • Joachims, T.1
  • 30
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • J. D. Thompson, D. G. Higgins and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 31
    • 0033537993 scopus 로고    scopus 로고
    • Genthreader: An efficient and reliable protein fold recognition method for genomic sequences
    • David T. Jones, Genthreader: An efficient and reliable protein fold recognition method for genomic sequences. Journal of Molecular Biology, 287:797-815, 1999.
    • (1999) Journal of Molecular Biology , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 32
    • 0035700864 scopus 로고    scopus 로고
    • Progress in predicting interresidue contacts of proteins with neural networks and correlated mutations
    • P. Fariselli, Olmea O., Valencia A. and Cassadio R., Progress in predicting interresidue contacts of proteins with neural networks and correlated mutations. Proteins: Struct., Funct., Genet., Suppl 5:157-162, 2001.
    • (2001) Proteins: Struct., Funct., Genet., Suppl , vol.5 , pp. 157-162
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Cassadio, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.