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Volumn 1, Issue 2, 2002, Pages 85-91

Hunting for "key residues" in the modeling of globular protein folding: An artificial neural network-based approach

Author keywords

Artificial neural network; Inverse protein folding; Key residues; Protein folding modeling; Protein structure prediction

Indexed keywords

ANGLE MEASUREMENT; COMPUTER SIMULATION; MOLECULAR STRUCTURE; NEURAL NETWORKS; TORSION TESTING;

EID: 33744743209     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2002.806914     Document Type: Article
Times cited : (2)

References (42)
  • 1
    • 0035039453 scopus 로고    scopus 로고
    • The birth of computational structural biology
    • M. Levitt, "The birth of computational structural biology," Nature. Structural Biol., vol. 8, no. 5, pp. 392-393, 2001.
    • (2001) Nature. Structural Biol. , vol.8 , Issue.5 , pp. 392-393
    • Levitt, M.1
  • 3
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • L. G. Presta and G. D. Rose, "Helix signals in proteins," Science, vol. 240, pp. 1632-1641, 1988.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 4
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of α-helices
    • J. S. Richardson and D. C. Richardson, "Amino acid preferences for specific locations at the ends of α-helices," Science, vol. 240, pp. 1648-1652, 1988.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 5
    • 0017868338 scopus 로고
    • Empirical predictions of protein conformation
    • [5] P. Y. Chou and G. D. Fasman, "Empirical predictions of protein conformation," Ann. Rev. Biochem., vol. 47, pp. 251-276, 1978.
    • (1978) Ann. Rev. Biochem. , vol.47 , pp. 251-276
    • Chou, P.Y.1    Fasman, G.D.2
  • 6
    • 0016162558 scopus 로고
    • Algorithms for prediction of α - Helical and β-structural regions in globular proteins
    • V. I. Lim, "Algorithms for prediction of α - helical and β-structural regions in globular proteins," J. Mol Biol., vol. 88, pp. 873-894, 1974.
    • (1974) J. Mol Biol. , vol.88 , pp. 873-894
    • Lim, V.I.1
  • 7
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • J. Garnier, D. J. Osguthorpe, and B. Robson, "Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins," J. Mol. Biol., vol. 120, pp. 97-120, 1978.
    • (1978) J. Mol. Biol. , vol.120 , pp. 97-120
    • Garnier, J.1    Osguthorpe, D.J.2    Robson, B.3
  • 8
    • 0024771475 scopus 로고
    • Pattern classification using neural networks
    • Nov.
    • R. Lippmann, "Pattern classification using neural networks," IEEE Commun. Mag., pp. 47-64, Nov. 1989.
    • (1989) IEEE Commun. Mag. , pp. 47-64
    • Lippmann, R.1
  • 9
    • 0023803244 scopus 로고
    • Predicting the secondary structure of globular proteins using neural network models
    • N. Qian and T. J. Sejnowski, "Predicting the secondary structure of globular proteins using neural network models," J. Mol. Biol., vol. 202, pp. 865-884, 1988.
    • (1988) J. Mol. Biol. , vol.202 , pp. 865-884
    • Qian, N.1    Sejnowski, T.J.2
  • 11
    • 0000268209 scopus 로고
    • Protein secondary structure prediction withaneuralnetwork
    • L. H. Holley and M. Karplus, "Protein secondary structure prediction withaneuralnetwork," Proc. Natl. Acad. Sci. USA, vol. 86, pp. 152-156, 1989.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 152-156
    • Holley, L.H.1    Karplus, M.2
  • 12
    • 0025334980 scopus 로고
    • Improvements in protein secondary structure prediction by an enhanced neural network
    • D. G. Kneller, F. E. Cohen, and R. Langridge, "Improvements in protein secondary structure prediction by an enhanced neural network," J. Mol Biol., vol. 214, pp. 171-182, 1990.
    • (1990) J. Mol Biol. , vol.214 , pp. 171-182
    • Kneller, D.G.1    Cohen, F.E.2    Langridge, R.3
  • 13
    • 0027690403 scopus 로고
    • Peptides secondary structure prediction with neural networks: A criterion for building appropriate learning sets
    • Nov.
    • C. Ruggiero, R. Sacile, and G. Rauch, "Peptides secondary structure prediction with neural networks: A criterion for building appropriate learning sets," IEEE Trans. Biomed. Eng., vol. 40, pp. 1114-1121, Nov. 1993.
    • (1993) IEEE Trans. Biomed. Eng. , vol.40 , pp. 1114-1121
    • Ruggiero, C.1    Sacile, R.2    Rauch, G.3
  • 14
    • 0035014847 scopus 로고    scopus 로고
    • Multi-class protein fold recognition using support vector machines and neural networks
    • C. H. Ding and I. Dubchak, "Multi-class protein fold recognition using support vector machines and neural networks," Bioinformatics, vol. 17, no. 4, pp. 349-358, 2001.
    • (2001) Bioinformatics , vol.17 , Issue.4 , pp. 349-358
    • Ding, C.H.1    Dubchak, I.2
  • 15
    • 0034887296 scopus 로고    scopus 로고
    • Prediction of protein functional domains from sequences using artificial neural networks
    • J. Murvai, K. Vlahovicek, C. Szepesvári, and S. Pongor, "Prediction of protein functional domains from sequences using artificial neural networks," Genome Res., vol. 11, no. 8, pp. 1410-1417, 2001.
    • (2001) Genome Res. , vol.11 , Issue.8 , pp. 1410-1417
    • Murvai, J.1    Vlahovicek, K.2    Szepesvári, C.3    Pongor, S.4
  • 16
    • 0035914053 scopus 로고    scopus 로고
    • Protein secondary structure: Category assignment and predictability
    • C. A. Andersen, H. Bohr, and S. Brunak, "Protein secondary structure: Category assignment and predictability," FEBS Lett., vol. 507, no. 1, pp. 6-10, 2001.
    • (2001) FEBS Lett. , vol.507 , Issue.1 , pp. 6-10
    • Andersen, C.A.1    Bohr, H.2    Brunak, S.3
  • 17
    • 0034753838 scopus 로고    scopus 로고
    • Identification of homology in protein structure classification
    • S. Dietmann and L. Holm, "Identification of homology in protein structure classification," Nature Structural Biol., vol. 8, no. 11, pp. 953-957, 2001.
    • (2001) Nature Structural Biol. , vol.8 , Issue.11 , pp. 953-957
    • Dietmann, S.1    Holm, L.2
  • 18
    • 0034780030 scopus 로고    scopus 로고
    • Peons: A neural-network-based consensus predictor that improves fold recognition
    • J. Lundström, L. Rychlewski, J. Bujnicki, and A. Elofsson, "Peons: A neural-network-based consensus predictor that improves fold recognition," Protein Sci., vol. 10, no. 11, pp. 2354-2362, 2001.
    • (2001) Protein Sci. , vol.10 , Issue.11 , pp. 2354-2362
    • Lundström, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 19
    • 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, vol. 47, no. 2, pp. 228-235, 2002.
    • (2002) Proteins , vol.47 , Issue.2 , pp. 228-235
    • Pollastri, G.1    Przybylski, D.2    Rost, B.3    Baldi, P.4
  • 20
    • 0001079105 scopus 로고
    • On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations
    • W. Kabsch and C. Sander, "On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations," Proc Natl Acad Sci USA, vol. 81, pp. 1075-1078, 1984.
    • (1984) Proc Natl Acad Sci USA , vol.81 , pp. 1075-1078
    • Kabsch, W.1    Sander, C.2
  • 21
    • 0027448801 scopus 로고
    • Origins of structural diversity within sequentially identical hexapeptides
    • B. I. Cohen, S. R. Presnell, and F. E. Cohen, "Origins of structural diversity within sequentially identical hexapeptides," Protein Sci., vol. 2, no. 12, pp. 2134-45, 1993.
    • (1993) Protein Sci. , vol.2 , Issue.12 , pp. 2134-2145
    • Cohen, B.I.1    Presnell, S.R.2    Cohen, F.E.3
  • 22
    • 0037154267 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a family of designed sequences
    • P. Koehl and M. Levitt, "Improved recognition of native-like protein structures using a family of designed sequences," Proc. Nat. Acad. Sci. USA, vol. 99, no. 2, pp. 691-696, 2002.
    • (2002) Proc. Nat. Acad. Sci. USA , vol.99 , Issue.2 , pp. 691-696
    • Koehl, P.1    Levitt, M.2
  • 23
    • 0032903975 scopus 로고    scopus 로고
    • Feasibility in the inverse protein folding protocol
    • M. Ota and K. Nishikawa, "Feasibility in the inverse protein folding protocol," Protein Sci., vol. 8, no. 5, pp. 1001-1009, 1999.
    • (1999) Protein Sci. , vol.8 , Issue.5 , pp. 1001-1009
    • Ota, M.1    Nishikawa, K.2
  • 24
    • 0031709922 scopus 로고    scopus 로고
    • Optimizing potentials for the inverse protein folding problem
    • T. L. Chiu and R. A. Goldstein, "Optimizing potentials for the inverse protein folding problem," Protein Eng., vol. 11, no. 9, pp. 749-752, 1998.
    • (1998) Protein Eng. , vol.11 , Issue.9 , pp. 749-752
    • Chiu, T.L.1    Goldstein, R.A.2
  • 27
    • 0029159770 scopus 로고
    • The structural repertoire of the human V kappa domain
    • I. M. Tomlinson, J. P. L. Cox, E. Gherardi, A. M. Lesk, and C. Chothia, 'The structural repertoire of the human V kappa domain," EMBO J., vol. 14, pp. 4628-4638, 1995.
    • (1995) EMBO J. , vol.14 , pp. 4628-4638
    • Tomlinson, I.M.1    Cox, J.P.L.2    Gherardi, E.3    Lesk, A.M.4    Chothia, C.5
  • 28
    • 0030589039 scopus 로고    scopus 로고
    • Structural families in loops of homologous proteins: Automatic classification, modeling and application to antibodies
    • A. C. Martin and J. M. Thornton, "Structural families in loops of homologous proteins: Automatic classification, modeling and application to antibodies," J Mol Biol., vol. 15, pp. 800-15, 1996.
    • (1996) J Mol Biol. , vol.15 , pp. 800-815
    • Martin, A.C.1    Thornton, J.M.2
  • 30
    • 0035254936 scopus 로고    scopus 로고
    • Conserved key amino acid positions (CKAAP's) derived from the analysis of common substructures in proteins
    • B. V. Reddy, W. W. Li, I. N. Shindyalov, and P. E. Bourne, "Conserved key amino acid positions (CKAAP's) derived from the analysis of common substructures in proteins," Proteins, vol. 42, pp. 148-163, 2001.
    • (2001) Proteins , vol.42 , pp. 148-163
    • Reddy, B.V.1    Li, W.W.2    Shindyalov, I.N.3    Bourne, P.E.4
  • 31
    • 0035175771 scopus 로고    scopus 로고
    • CKAAP's DB: A conserved key amino acid positions database
    • W. W. Li, B. V. Reddy, I. N. Shindyalov, and P. E. Bourne, "CKAAP's DB: A conserved key amino acid positions database," Nucleic Acids Res., vol. 29, pp. 329-331, 2001.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 329-331
    • Li, W.W.1    Reddy, B.V.2    Shindyalov, I.N.3    Bourne, P.E.4
  • 32
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • J. Overington, M. S. Johnson, A. Sali, and T. L. Blundell, "Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction," Proc. Roy. Soc. Land. B. Biol. Sci., vol. 241, pp. 132-45, 1990.
    • (1990) Proc. Roy. Soc. Land. B. Biol. Sci. , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 33
    • 0034257020 scopus 로고    scopus 로고
    • Key residues approach to the definition of protein families and analysis of sparse family signatures
    • J. C. Ison, M. J. Blades, A. J. Bleasby, S. C. Daniel, J. H. Parish, and J. B. Findlay, "Key residues approach to the definition of protein families and analysis of sparse family signatures," Proteins, vol. 40, pp. 330-41, 2000.
    • (2000) Proteins , vol.40 , pp. 330-341
    • Ison, J.C.1    Blades, M.J.2    Bleasby, A.J.3    Daniel, S.C.4    Parish, J.H.5    Findlay, J.B.6
  • 34
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • M. Vendruscolo, E. Paci, C. M. Dobson, and M. Karplus, "Three key residues form a critical contact network in a protein folding transition state," Nature, vol. 409, pp. 641-645, 2001.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 35
    • 0017157584 scopus 로고
    • A simplified representation of protein conformation forrapid simulation of protein folding
    • M. Levitt, "A simplified representation of protein conformation forrapid simulation of protein folding," J. Mol. Biol., vol. 104, pp. 59-107, 1976.
    • (1976) J. Mol. Biol. , vol.104 , pp. 59-107
    • Levitt, M.1
  • 36
    • 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, vol. 18, pp. 2577-2637, 1983.
    • (1983) Biopolymers , vol.18 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 37
    • 0022471098 scopus 로고
    • Learning representations by back-propagating errors
    • D. E. Rumelhart, O. E. Hinton, and R. J. Williams, "Learning representations by back-propagating errors," Nature, vol. 323, pp. 533-536, 1986.
    • (1986) Nature , vol.323 , pp. 533-536
    • Rumelhart, D.E.1    Hinton, O.E.2    Williams, R.J.3
  • 38
    • 0028984808 scopus 로고
    • Prediction of hypervariable CDR-H3 loop structures in antibodies
    • M. Reczko, A. Martin, H. Bohr, and S. Suhai, "Prediction of hypervariable CDR-H3 loop structures in antibodies," Protein Eng., vol. 8, pp. 389-395, 1995.
    • (1995) Protein Eng. , vol.8 , pp. 389-395
    • Reczko, M.1    Martin, A.2    Bohr, H.3    Suhai, S.4
  • 39
    • 0017709445 scopus 로고
    • Beta-turns in proteins
    • P. Y. Chou and G. D. Fasman, "Beta-turns in proteins," J. Mol. Biol., vol. 115, pp. 135-175, 1977.
    • (1977) J. Mol. Biol. , vol.115 , pp. 135-175
    • Chou, P.Y.1    Fasman, G.D.2
  • 41
    • 0027102226 scopus 로고
    • OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
    • J. Heringa, H. Sommerfeldt, D. Higgins, and P. Argos, "OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity," CABIOS, vol. 8, pp. 599-600, 1992.
    • (1992) CABIOS , vol.8 , pp. 599-600
    • Heringa, J.1    Sommerfeldt, H.2    Higgins, D.3    Argos, P.4
  • 42
    • 0029564871 scopus 로고
    • A 3D sequence-independent representation of the protein bank
    • D. Fisher, C. J. Tsai, R. Nussinov, and H. Wolfson, "A 3D sequence-independent representation of the protein bank," Protein Eng., vol. 8, pp. 981-997, 1995.
    • (1995) Protein Eng. , vol.8 , pp. 981-997
    • Fisher, D.1    Tsai, C.J.2    Nussinov, R.3    Wolfson, H.4


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