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Volumn , Issue , 2007, Pages 153-181

DISTILL: A MACHINE LEARNING APPROACH TO AB INITIO PROTEIN STRUCTURE PREDICTION

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EID: 85196442690     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789812708892_0007     Document Type: Chapter
Times cited : (6)

References (47)
  • 1
    • 0032828469 scopus 로고    scopus 로고
    • Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
    • C. A. Orengo, J. E. Bray, T. Hubbard, L. Lo Conte and I. I. Sillitoe, Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction, Proteins: Structure, Function and Genetics 37(S3), 149-170 (1999).
    • (1999) Proteins: Structure, Function and Genetics , vol.37 , Issue.S3 , pp. 149-170
    • Orengo, C.A.1    Bray, J.E.2    Hubbard, T.3    Lo Conte, L.4    Sillitoe, I.I.5
  • 2
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, function and genetics
    • A. M. Lesk, L. Lo Conte and T. J. P. Hubbard, Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, function and genetics, Proteins: Structure, Function and Genetics S5, 98-118 (2001).
    • (2001) Proteins: Structure, Function and Genetics , vol.S5 , pp. 98-118
    • Lesk, A.M.1    Lo Conte, L.2    Hubbard, T.J.P.3
  • 3
    • 0242267517 scopus 로고    scopus 로고
    • Critical assessment ofmethods of protein structure prediction (casp)-round v
    • J. Moult, K. Fidelis,A. Zemla and T.Hubbard, Critical assessment ofmethods of protein structure prediction (casp)-round v, Proteins 53(S6), 334-339 (2003).
    • (2003) Proteins , vol.53 , Issue.S6 , pp. 334-339
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 4
    • 85196442482 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (casp)-round vi
    • Epub 26 September, (in press)
    • J. Moult, K. Fidelis, A. Tramontano, B. Rost and T. Hubbard, Critical assessment of methods of protein structure prediction (casp)-round vi, Proteins, Epub 26 September 2005 (in press).
    • (2005) Proteins
    • Moult, J.1    Fidelis, K.2    Tramontano, A.3    Rost, B.4    Hubbard, T.5
  • 6
    • 30344487561 scopus 로고    scopus 로고
    • Assessment of casp6 predictions for new and nearly new fold targets
    • Epub 26 September, (in press)
    • J. J. Vincent, C. H. Tai, B. K. Sathyanarayana and B. Lee, Assessment of casp6 predictions for new and nearly new fold targets, Proteins, Epub 26 September 2005 (in press).
    • (2005) Proteins
    • Vincent, J.J.1    Tai, C.H.2    Sathyanarayana, B.K.3    Lee, B.4
  • 8
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • D. T. Jones, Protein secondary structure prediction based on position-specific scoring matrices, J. Mol. Biol. 292, 195-202 (1999).
    • (1999) J. Mol. Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 9
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • B. Rost and C. Sander, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol. 232, 584-599 (1993).
    • (1993) J. Mol. Biol , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 10
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • G. Pollastri, D. Przybylski, B. Rost and P. Baldi, Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles, Proteins 47, 228-235 (2002).
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 11
    • 17444397116 scopus 로고    scopus 로고
    • Porter: A new, accurate server for protein secondary structure prediction
    • G. Pollastri and A. McLysaght, Porter: a new, accurate server for protein secondary structure prediction, Bioinformatics 21(8), 1719-1720 (2005).
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1719-1720
    • Pollastri, G.1    McLysaght, A.2
  • 12
    • 0030627407 scopus 로고    scopus 로고
    • Recovery of protein structure from contact maps
    • M. Vendruscolo, E. Kussell and E. Domany, Recovery of protein structure from contact maps, Folding and Design 2, 295-306 (1997).
    • (1997) Folding and Design , vol.2 , pp. 295-306
    • Vendruscolo, M.1    Kussell, E.2    Domany, E.3
  • 13
    • 0033537993 scopus 로고    scopus 로고
    • Genthreader: An efficient and reliable protein fold recognition method for genomic sequences
    • D. T. Jones, Genthreader: an efficient and reliable protein fold recognition method for genomic sequences, J. Mol. Biol. 287, 797-815 (1999).
    • (1999) J. Mol. Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 15
    • 0030801002 scopus 로고    scopus 로고
    • Gapped blast and psi-blast: A new generation of protein database search programs
    • S. F. Altschul, T. L. Madden and A. A. Schaffer, Gapped blast and psi-blast: a new generation of protein database search programs, Nucl. Acids Res. 25, 3389-3402 (1997).
    • (1997) Nucl. Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 17
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • B. Rost and C. Sander, Conservation and prediction of solvent accessibility in protein families, Proteins: Structure, Function and Genetics 20, 216-226 (1994).
    • (1994) Proteins: Structure, Function and Genetics , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 20
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignments profiles to improve protein secondary structure prediction
    • J. A. Cuff and G. J. Barton, Application of multiple sequence alignments profiles to improve protein secondary structure prediction, Proteins: Structure, Function and Genetics 40, 502-511 (2000).
    • (2000) Proteins: Structure, Function and Genetics , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 21
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • G. Pollastri, P. Fariselli, R. Casadio and P. Baldi, Prediction of coordination number and relative solvent accessibility in proteins, Proteins 47, 142-235 (2002).
    • (2002) Proteins , vol.47 , pp. 142-235
    • Pollastri, G.1    Fariselli, P.2    Casadio, R.3    Baldi, P.4
  • 23
    • 3142558004 scopus 로고    scopus 로고
    • Reconstruction of protein structures from a vectorial representation
    • M. Porto, U. Bastolla, H. E. Roman and M. Vendruscolo, Reconstruction of protein structures from a vectorial representation, Phys. Rev. Lett. 92, 218101 (2004).
    • (2004) Phys. Rev. Lett , vol.92 , pp. 218101
    • Porto, M.1    Bastolla, U.2    Roman, H.E.3    Vendruscolo, M.4
  • 24
    • 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 , pp. S62-S70
    • Pollastri, G.1    Baldi, P.2
  • 25
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • L. Holm and C. Sander, Parser for protein folding units, Proteins 19, 256-268 (1994).
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 27
    • 0035700864 scopus 로고    scopus 로고
    • Progress in predicting inter-residue contacts of proteins with neural networks and correlatedmutations
    • P. Fariselli, O. Olmea, A. Valencia and R. Casadio, Progress in predicting inter-residue contacts of proteins with neural networks and correlatedmutations, Proteins: Structure,Function and Genetics S5, 157-162 (2001).
    • (2001) Proteins: Structure,Function and Genetics , vol.S5 , pp. 157-162
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 28
    • 33745610096 scopus 로고    scopus 로고
    • A two-stage approach for improved prediction of residue contact maps
    • A. Vullo, I. Walsh and G. Pollastri, A two-stage approach for improved prediction of residue contact maps, BMC Bioinformatics 7, 180 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 180
    • Vullo, A.1    Walsh, I.2    Pollastri, G.3
  • 29
    • 0033047710 scopus 로고    scopus 로고
    • Neural network based predictor of residue contacts in proteins
    • P. Fariselli and R. Casadio, Neural network based predictor of residue contacts in proteins, Protein Engineering 12, 15-21 (1999).
    • (1999) Protein Engineering , vol.12 , pp. 15-21
    • Fariselli, P.1    Casadio, R.2
  • 30
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • P. Fariselli, O. Olmea, A. Valencia and R. Casadio, Prediction of contact maps with neural networks and correlated mutations, Protein Engineering 14(11), 439-835 (2001).
    • (2001) Protein Engineering , vol.14 , Issue.11 , pp. 439-835
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 31
    • 2542420004 scopus 로고    scopus 로고
    • The principled design of large-scale recursive neural network architectures - DAG-RNNS and the protein structure prediction problem
    • P. Baldi and G. Pollastri, The principled design of large-scale recursive neural network architectures - DAG-RNNS and the protein structure prediction problem. Journal of Machine Learning Research 4, 575-602 (2003).
    • (2003) Journal of Machine Learning Research , vol.4 , pp. 575-602
    • Baldi, P.1    Pollastri, G.2
  • 32
    • 0001691450 scopus 로고    scopus 로고
    • Protein fold determination from sparse distance restraints: The restrained generic protein direct Monte Carlo method
    • D.A.Debe,M. J.Carlson, J. Sadanobu, S. I.Chan andW.A.Goddard, Protein fold determination from sparse distance restraints: the restrained generic protein direct Monte Carlo method, J. Phys. Chem. 103, 3001-3008 (1999).
    • (1999) J. Phys. Chem , vol.103 , pp. 3001-3008
    • Debe, D.A.1    Carlson, M.J.2    Sadanobu, J.3    Chan, S.I.4    Goddard, W.A.5
  • 33
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • A. Aszodi, M. J. Gradwell and W. R. Taylor, Global fold determination from a small number of distance restraints, J. Mol. Biol. 251, 308-326 (1995).
    • (1995) J. Mol. Biol , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 34
    • 0033516514 scopus 로고    scopus 로고
    • Ab initiofold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
    • E. S. Huang, R. Samudrala and J. W. Ponder, Ab initiofold prediction of small helical proteins using distance geometry and knowledge-based scoring functions, J. Mol. Biol. 290, 267-281 (1999).
    • (1999) J. Mol. Biol , vol.290 , pp. 267-281
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 35
    • 0031575423 scopus 로고    scopus 로고
    • Monsster: A method for folding globular proteins with a small number of distance restraints
    • J. Skolnick, A. Kolinski and A. R. Ortiz, Monsster: a method for folding globular proteins with a small number of distance restraints, J. Mol. Biol. 265 (1997) 217-241.
    • (1997) J. Mol. Biol , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 36
    • 0034501067 scopus 로고    scopus 로고
    • De novo protein structure determination using sparse NMR data
    • P. M. Bowers, C. E. Strauss and D. Baker, De novo protein structure determination using sparse NMR data. J. Biomol. NMR 18, 311-318 (2000).
    • (2000) J. Biomol. NMR , vol.18 , pp. 311-318
    • Bowers, P.M.1    Strauss, C.E.2    De Baker3
  • 38
    • 24744453057 scopus 로고    scopus 로고
    • Striped sheets and protein contact prediction
    • R. M. McCallum, Striped sheets and protein contact prediction. Bioinformatics 20 (Suppl. 1), 224-231 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 224-231
    • McCallum, R.M.1
  • 39
    • 85196464638 scopus 로고    scopus 로고
    • Casp6 home page.
  • 41
    • 33744487993 scopus 로고    scopus 로고
    • Modular DAG-RNN architectures for assembling coarse protein structures
    • G. Pollastri, A. Vullo, P. Frasconi and P. Baldi, Modular DAG-RNN architectures for assembling coarse protein structures, Journal ofComputational Biology 13(3), 631-650 (2006).
    • (2006) Journal ofComputational Biology , vol.13 , Issue.3 , pp. 631-650
    • Pollastri, G.1    Vullo, A.2    Frasconi, P.3    Baldi, P.4
  • 43
    • 0032165969 scopus 로고    scopus 로고
    • A general framework for adaptive processing of data structures
    • P. Frasconi, M. Gori and A. Sperduti, A general framework for adaptive processing of data structures. IEEE Trans. on Neural Networks 9, 768-786 (1998).
    • (1998) IEEE Trans. on Neural Networks , vol.9 , pp. 768-786
    • Frasconi, P.1    Gori, M.2    Sperduti, A.3
  • 44
    • 0033369033 scopus 로고    scopus 로고
    • Exploiting the past and the future in protein secondary structure prediction
    • P. Baldi, S. Brunak, P. Frasconi, G. Soda and G. Pollastri, Exploiting the past and the future in protein secondary structure prediction, Bioinformatics 15, 937-946 (1999).
    • (1999) Bioinformatics , vol.15 , pp. 937-946
    • Baldi, P.1    Brunak, S.2    Frasconi, P.3    Soda, G.4    Pollastri, G.5
  • 45
    • 1842455284 scopus 로고    scopus 로고
    • Disulfide connectivity prediction using recursive neural networks and evolutionary information
    • A. Vullo and P. Frasconi, Disulfide connectivity prediction using recursive neural networks and evolutionary information, Bioinformatics 20(5), 653-659 (2004).
    • (2004) Bioinformatics , vol.20 , Issue.5 , pp. 653-659
    • Vullo, A.1    Frasconi, P.2
  • 46
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch and C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577-2637 (1983).
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 47
    • 26944482741 scopus 로고    scopus 로고
    • Learning protein secondary structure from sequential and relational data
    • A. Ceroni, P. Frasconi and G. Pollastri, Learning protein secondary structure from sequential and relational data, Neural Networks 18(8), 1029-1039 (2005).
    • (2005) Neural Networks , vol.18 , Issue.8 , pp. 1029-1039
    • Ceroni, A.1    Frasconi, P.2    Pollastri, G.3


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