메뉴 건너뛰기




Volumn 33, Issue 18, 2017, Pages 2842-2849

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT;

EID: 85026373829     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx218     Document Type: Article
Times cited : (277)

References (54)
  • 2
    • 4043052866 scopus 로고    scopus 로고
    • Accurate prediction of solvent accessibility using neural networks-based regression
    • Adamczak,R. et al. (2004) Accurate prediction of solvent accessibility using neural networks-based regression. Proteins, 56, 753-767.
    • (2004) Proteins , vol.56 , pp. 753-767
    • Adamczak, R.1
  • 3
    • 0037340834 scopus 로고    scopus 로고
    • Real value prediction of solvent accessibility from amino acid sequence
    • Ahmad,S. et al. (2003) Real value prediction of solvent accessibility from amino acid sequence. Proteins, 50, 629-635.
    • (2003) Proteins , vol.50 , pp. 629-635
    • Ahmad, S.1
  • 4
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 6
    • 0033369033 scopus 로고    scopus 로고
    • Exploiting the past and the future in protein secondary structure prediction
    • Baldi,P. et al. (1999) Exploiting the past and the future in protein secondary structure prediction. Bioinformatics, 15, 937-946.
    • (1999) Bioinformatics , vol.15 , pp. 937-946
    • Baldi, P.1
  • 7
    • 84869761071 scopus 로고    scopus 로고
    • The protein-folding problem, 50 years on
    • Dill,K.A., and MacCallum,J.L. (2012) The protein-folding problem, 50 years on. Science, 338, 1042-1046.
    • (2012) Science , vol.338 , pp. 1042-1046
    • Dill, K.A.1    MacCallum, J.L.2
  • 8
    • 34249914807 scopus 로고    scopus 로고
    • Real-SPINE: An integrated system of neural networks for real-value prediction of protein structural properties
    • Dor,O., and Zhou,Y. (2007) Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties. Protein, 68, 76-81.
    • (2007) Protein , vol.68 , pp. 76-81
    • Dor, O.1    Zhou, Y.2
  • 9
    • 84979854249 scopus 로고    scopus 로고
    • JPred4: A protein secondary structure prediction server
    • Drozdetskiy,A. et al. (2015) JPred4: a protein secondary structure prediction server. Nucleic Acids Res., 43, W389-W394.
    • (2015) Nucleic Acids Res. , vol.43 , pp. W389-W394
    • Drozdetskiy, A.1
  • 10
    • 83855162773 scopus 로고    scopus 로고
    • SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
    • Faraggi,E. et al. (2012) SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J. Comput. Chem., 33, 259-267.
    • (2012) J. Comput. Chem. , vol.33 , pp. 259-267
    • Faraggi, E.1
  • 11
    • 0023731964 scopus 로고
    • Amino acid side chain parameters for correlation studies in biology and pharmacology
    • Fauchère,J.L. et al. (1988) Amino acid side chain parameters for correlation studies in biology and pharmacology. Int. J. Pept. Protein Res., 32, 269-278.
    • (1988) Int. J. Pept. Protein Res. , vol.32 , pp. 269-278
    • Fauchère, J.L.1
  • 12
    • 26444473604 scopus 로고    scopus 로고
    • Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure
    • Garg,A. et al. (2005) Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure. Proteins, 61, 318-324.
    • (2005) Proteins , vol.61 , pp. 318-324
    • Garg, A.1
  • 13
    • 0014116254 scopus 로고
    • Minimization of polypeptide energy i. Preliminary structures of bovine pancreatic ribonuclease s-peptide
    • Gibson,K.D., and Scheraga,H.A. (1967) Minimization of polypeptide energy. i. preliminary structures of bovine pancreatic ribonuclease s-peptide. Proc. Natl. Acad. Sci. USA, 58, 420-427.
    • (1967) Proc. Natl. Acad. Sci. USA , vol.58 , pp. 420-427
    • Gibson, K.D.1    Scheraga, H.A.2
  • 14
    • 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
    • Gilis,D., and Rooman,M. (1997) 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) J. Mol. Biol. , vol.272 , pp. 276-290
    • Gilis, D.1    Rooman, M.2
  • 15
    • 71249112130 scopus 로고    scopus 로고
    • Offline handwriting recognition with multidimensional recurrent neural networks
    • In: Koller D., Schuurmans D., Bengio Y., and Bottou L., editors, Curran Associates, Inc., Red Hook, NY
    • Graves,A., and Schmidhuber,J. (2009) Offline handwriting recognition with multidimensional recurrent neural networks. In: Koller D., Schuurmans D., Bengio Y., and Bottou L., editors, Advances in Neural Information Processing Systems 21. Curran Associates, Inc., Red Hook, NY, p.545-552.
    • (2009) Advances in Neural Information Processing Systems , vol.21 , pp. 545-552
    • Graves, A.1    Schmidhuber, J.2
  • 16
    • 14644400399 scopus 로고    scopus 로고
    • An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
    • Hamelryck,T. (2005) An amino acid has two sides: a new 2D measure provides a different view of solvent exposure. Proteins, 59, 38-48.
    • (2005) Proteins , vol.59 , pp. 38-48
    • Hamelryck, T.1
  • 17
    • 85017102714 scopus 로고    scopus 로고
    • Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks
    • Hanson,J. et al. (2017) Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinformatics, 33, 685-692.
    • (2017) Bioinformatics , vol.33 , pp. 685-692
    • Hanson, J.1
  • 18
    • 84934966065 scopus 로고    scopus 로고
    • Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning
    • Heffernan,R. et al. (2015) Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. Sci. Rep., 5, 11476.
    • (2015) Sci. Rep. , vol.5 , pp. 11476
    • Heffernan, R.1
  • 19
    • 84962199140 scopus 로고    scopus 로고
    • Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins
    • Heffernan, R. et al. (2016) Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinformatics, 32, 843-849.
    • (2016) Bioinformatics , vol.32 , pp. 843-849
    • Heffernan, R.1
  • 21
    • 0025039476 scopus 로고
    • Predicting surface exposure of amino acids from protein sequence
    • Holbrook,S.R. et al. (1990) Predicting surface exposure of amino acids from protein sequence. Protein Eng., 3, 659-665.
    • (1990) Protein Eng. , vol.3 , pp. 659-665
    • Holbrook, S.R.1
  • 22
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on positionspecific scoring matrices
    • Jones,D.T. (1999) Protein secondary structure prediction based on positionspecific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch,W., and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 24
    • 0027407722 scopus 로고
    • Estimation and use of protein backbone angle probabilities
    • Kang,H.S. et al. (1993) Estimation and use of protein backbone angle probabilities. J Mol. Biol., 229, 448-460.
    • (1993) J Mol. Biol. , vol.229 , pp. 448-460
    • Kang, H.S.1
  • 26
    • 33749357045 scopus 로고    scopus 로고
    • CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
    • Kinjo,A.R., and Nishikawa,K. (2006) CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks. BMC Bioinformatics, 7, 401.
    • (2006) BMC Bioinformatics , vol.7 , pp. 401
    • Kinjo, A.R.1    Nishikawa, K.2
  • 27
    • 3543101355 scopus 로고    scopus 로고
    • Protein backbone angle prediction with machine learning approaches
    • Kuang,R. et al. (2004) Protein backbone angle prediction with machine learning approaches. Bioinformatics, 20, 1612-1621.
    • (2004) Bioinformatics , vol.20 , pp. 1612-1621
    • Kuang, R.1
  • 28
    • 35148893484 scopus 로고    scopus 로고
    • A tutorial on energy-based learning
    • In: Bakir, G., Hofman, T., Schölkopf, B., Smola, A., Taskar, B. (eds.) MIT Press, Cambridge
    • LeCun,Y. et al. (2006) A tutorial on energy-based learning. In: Bakir, G., Hofman, T., Schölkopf, B., Smola, A., Taskar, B. (eds.) Predicting Structured Data. MIT Press, Cambridge.
    • (2006) Predicting Structured Data
    • LeCun, Y.1
  • 29
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee,B., and Richards,F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 30
    • 84927770389 scopus 로고    scopus 로고
    • Predicting backbone ca angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network
    • Lyons,J. et al. (2014) Predicting backbone ca angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J. Comput. Chem., 35, 2040-2046.
    • (2014) J. Comput. Chem. , vol.35 , pp. 2040-2046
    • Lyons, J.1
  • 31
    • 84907487648 scopus 로고    scopus 로고
    • SSpro/ACCpro 5: Almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity
    • Magnan,C.N., and Baldi,P. (2014) SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. Bioinformatics, 30, 2592-2597.
    • (2014) Bioinformatics , vol.30 , pp. 2592-2597
    • Magnan, C.N.1    Baldi, P.2
  • 32
    • 84880998440 scopus 로고    scopus 로고
    • Porter, PaleAle 4.0: High-accuracy prediction of protein secondary structure and relative solvent accessibility
    • Mirabello,C., and Pollastri,G. (2013) Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility. Bioinformatics, 29, 2056-2058.
    • (2013) Bioinformatics , vol.29 , pp. 2056-2058
    • Mirabello, C.1    Pollastri, G.2
  • 33
    • 76549252207 scopus 로고
    • The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain
    • Pauling,L. et al. (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA, 37, 205-211.
    • (1951) Proc. Natl. Acad. Sci. USA , vol.37 , pp. 205-211
    • Pauling, L.1
  • 34
    • 0036568279 scopus 로고    scopus 로고
    • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
    • Pollastri,G. et al. (2002a) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-235.
    • (2002) Proteins , vol.47 , pp. 228-235
    • Pollastri, G.1
  • 35
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • Pollastri,G. et al. (2002b) Prediction of coordination number and relative solvent accessibility in proteins. Proteins, 47, 142-153.
    • (2002) Proteins , vol.47 , pp. 142-153
    • Pollastri, G.1
  • 36
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: Lightning-fast iterative protein sequence searching by HMM-HMMalignment
    • Remmert,M. et al. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMMalignment. Nat. Methods, 9, 173-175.
    • (2012) Nat. Methods , vol.9 , pp. 173-175
    • Remmert, M.1
  • 37
    • 0000939821 scopus 로고    scopus 로고
    • What is the probability of a chance prediction of a protein structure with an rmsd of 6A
    • Reva,B.A. et al. (1998) What is the probability of a chance prediction of a protein structure with an rmsd of 6A. Fold Des., 3, 141-147.
    • (1998) Fold Des. , vol.3 , pp. 141-147
    • Reva, B.A.1
  • 38
    • 0035782925 scopus 로고    scopus 로고
    • Review: Protein secondary structure prediction continues to rise
    • Rost,B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol., 134, 204-218.
    • (2001) J. Struct. Biol. , vol.134 , pp. 204-218
    • Rost, B.1
  • 39
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost,B., and Sander,C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226.
    • (1994) Proteins , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 41
    • 46249133956 scopus 로고    scopus 로고
    • HSEpred: Predict half-sphere exposure from protein sequences
    • Song,J. et al. (2008) HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics, 24, 1489-1497.
    • (2008) Bioinformatics , vol.24 , pp. 1489-1497
    • Song, J.1
  • 42
    • 84904163933 scopus 로고    scopus 로고
    • Dropout: A simple way to prevent neural networks from overfitting
    • Srivastava,N. et al. (2014) Dropout: a simple way to prevent neural networks from overfitting. J. Mach. Learn. Res., 15, 1929-1958.
    • (2014) J. Mach. Learn. Res. , vol.15 , pp. 1929-1958
    • Srivastava, N.1
  • 43
    • 84878402147 scopus 로고    scopus 로고
    • LSTM neural networks for language modeling
    • Sundermeyer,M. et al. (2012) LSTM neural networks for language modeling. In: Proceedings Interspeech. p.194-197.
    • (2012) Proceedings Interspeech , pp. 194-197
    • Sundermeyer, M.1
  • 44
    • 66349094681 scopus 로고    scopus 로고
    • Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy
    • Tuncbag,N. et al. (2009) Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics, 25, 1513-1520.
    • (2009) Bioinformatics , vol.25 , pp. 1513-1520
    • Tuncbag, N.1
  • 45
    • 84954113329 scopus 로고    scopus 로고
    • Protein secondary structure prediction using deep convolutional neural fields
    • Wang,S. et al. (2016) Protein secondary structure prediction using deep convolutional neural fields. Sci. Rep., 6, 18962.
    • (2016) Sci. Rep. , vol.6 , pp. 18962
    • Wang, S.1
  • 46
    • 17844373552 scopus 로고    scopus 로고
    • Protein secondary structure prediction with dihedral angles
    • Wood,M.J., and Hirst,J.D. (2005) Protein secondary structure prediction with dihedral angles. Proteins, 59, 476-481.
    • (2005) Proteins , vol.59 , pp. 476-481
    • Wood, M.J.1    Hirst, J.D.2
  • 48
    • 44949201613 scopus 로고    scopus 로고
    • Real-value prediction of backbone torsion angles
    • Xue,B. et al. (2008) Real-value prediction of backbone torsion angles. Proteins, 72, 427-433.
    • (2008) Proteins , vol.72 , pp. 427-433
    • Xue, B.1
  • 49
    • 85041440357 scopus 로고    scopus 로고
    • Sixty-five years of long March in protein secondary structure prediction: The final stretch?
    • Yang,Y. et al. (2016) Sixty-five years of long march in protein secondary structure prediction: the final stretch? Brief. Bioinform., DOI: 10.1093/bib/bbw129.
    • (2016) Brief. Bioinform
    • Yang, Y.1
  • 50
    • 84896921968 scopus 로고    scopus 로고
    • Context-based features enhance protein secondary structure prediction accuracy
    • Yaseen,A., and Li,Y. (2014) Context-based features enhance protein secondary structure prediction accuracy. J. Chem. Inf. Model., 54, 992-1002.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 992-1002
    • Yaseen, A.1    Li, Y.2
  • 51
    • 27644490770 scopus 로고    scopus 로고
    • Better prediction of protein contact number using a support vector regression analysis of amino acid sequence
    • Yuan,Z. (2005) Better prediction of protein contact number using a support vector regression analysis of amino acid sequence. BMC Bioinformatics, 6, 248.
    • (2005) BMC Bioinformatics , vol.6 , pp. 248
    • Yuan, Z.1
  • 52
    • 6344258643 scopus 로고    scopus 로고
    • Prediction of protein accessible surface areas by support vector regression
    • Yuan,Z., and Huang,B. (2004) Prediction of protein accessible surface areas by support vector regression. Proteins, 57, 558-564.
    • (2004) Proteins , vol.57 , pp. 558-564
    • Yuan, Z.1    Huang, B.2
  • 53
    • 84878372856 scopus 로고    scopus 로고
    • Prediction of one-dimensional structural properties of proteins by integrated neural networks
    • In: Rangwala, R. and Karypis, G. (ed.) Chap. 4, John Wiley & Sons, Inc., Hoboken, NJ
    • Zhou,Y., and Faraggi,E. (2010) Prediction of one-dimensional structural properties of proteins by integrated neural networks. In: Rangwala, R. and Karypis, G. (ed.) Introduction to Protein Structure Prediction, Chap. 4, John Wiley & Sons, Inc., Hoboken, NJ. p.45-74.
    • (2010) Introduction to Protein Structure Prediction , pp. 45-74
    • Zhou, Y.1    Faraggi, E.2
  • 54
    • 79251601609 scopus 로고    scopus 로고
    • Trends in template/fragment-free protein structure prediction
    • Zhou,Y. et al. (2011) Trends in template/fragment-free protein structure prediction. Theor. Chem. Acc., 128, 3-16.
    • (2011) Theor. Chem. Acc. , vol.128 , pp. 3-16
    • Zhou, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.