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Volumn 5, Issue 4, 2016, Pages 211-216

Oversampling negative class improves contact map prediction

Author keywords

Contact maps; Contact maps prediction; Decision trees; Neural networks

Indexed keywords

ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER ANALYSIS; CONTACT MAP PREDICTION; DECISION TREE; DIAGNOSTIC TEST ACCURACY STUDY; LEARNING ALGORITHM; MACHINE LEARNING; MATHEMATICAL PARAMETERS; MEASUREMENT ACCURACY; NONHUMAN; PREDICTIVE VALUE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEOMICS; SENSITIVITY AND SPECIFICITY;

EID: 85042307211     PISSN: 22785221     EISSN: None     Source Type: Journal    
DOI: 10.18178/ijpmbs.5.4.211-216     Document Type: Article
Times cited : (1)

References (28)
  • 1
    • 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., vol. 292, pp. 195-202, 1999.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 2
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • R. Adamczak, A. Porollo, and J. Meller, "Combining prediction of secondary structure and solvent accessibility in proteins," Proteins Struct. Funct. Genet., vol. 59, pp. 467-475, 2005.
    • (2005) Proteins Struct. Funct. Genet. , vol.59 , pp. 467-475
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 3
    • 4043052866 scopus 로고    scopus 로고
    • Accurate prediction of solvent accessibility using neural networks-based regression
    • R. Adamczak, A. Porollo, and J. Meller, "Accurate prediction of solvent accessibility using neural networks-based regression," Proteins Struct. Funct. Genet., vol. 56, pp. 753-767, 2004.
    • (2004) Proteins Struct. Funct. Genet. , vol.56 , pp. 753-767
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 4
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • G. Pollastri, P. Baldi, P. Fariselli, and R. Casadio, "Prediction of coordination number and relative solvent accessibility in proteins," Proteins, vol. 47, pp. 142-153, 2002.
    • (2002) Proteins , vol.47 , pp. 142-153
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 5
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • J. Cheng and P. Baldi, "Improved residue contact prediction using support vector machines and a large feature set," BMC Bioinformatics, vol. 8, no. 2, 2007.
    • (2007) BMC Bioinformatics , vol.8 , Issue.2
    • Cheng, J.1    Baldi, P.2
  • 6
    • 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, vol. 7, no. 7, 2006.
    • (2006) BMC Bioinformatics , vol.7 , Issue.7
    • Vullo, A.1    Walsh, I.2    Pollastri, G.3
  • 7
    • 0032613288 scopus 로고    scopus 로고
    • Ab initio folding of proteins using restraints derived from evolutionary information
    • A. R. Ortiz, A. Kolinski, P. Rotkiewicz, B. Ilkowski, and J. Skolnick, "Ab initio folding of proteins using restraints derived from evolutionary information," Proteins, pp. 177-185, 1999.
    • (1999) Proteins , pp. 177-185
    • Ortiz, A.R.1    Kolinski, A.2    Rotkiewicz, P.3    Ilkowski, B.4    Skolnick, J.5
  • 8
    • 77951104043 scopus 로고    scopus 로고
    • Reducing phylogenetic bias in correlated mutation analysis
    • H. Ashkenazy and Y. Kliger, "Reducing phylogenetic bias in correlated mutation analysis," Protein Eng. Des. Sel., vol. 23, pp. 321-326, 2010.
    • (2010) Protein Eng. Des. Sel. , vol.23 , pp. 321-326
    • Ashkenazy, H.1    Kliger, Y.2
  • 9
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • U. Göbel, C. Sander, R. Schneider, and A. Valencia, "Correlated mutations and residue contacts in proteins," Proteins, vol. 18, pp. 309-317, 1994.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Göbel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 10
    • 84856090271 scopus 로고    scopus 로고
    • PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • D. T. Jones, D. W. A. Buchan, D. Cozzetto, and M. Pontil, "PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments," Bioinformatics, vol. 28, pp. 184-190, 2012.
    • (2012) Bioinformatics , vol.28 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.A.2    Cozzetto, D.3    Pontil, M.4
  • 11
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • S. F. Altschul, et al., "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs," Nucleic Acids Res., vol. 25, pp. 3389-3402, 1997.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 12
    • 0041719954 scopus 로고    scopus 로고
    • Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
    • G. Pollastri and P. Baldi, "Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners," Bioinformatics, vol. 18, pp. S62-S70, 2002.
    • (2002) Bioinformatics , vol.18 , pp. S62-S70
    • Pollastri, G.1    Baldi, P.2
  • 13
    • 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 Eng., vol. 14, pp. 835-843, 2001.
    • (2001) Protein Eng. , vol.14 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 14
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    • I. N. Shindyalov, N. A. Kolchanov, and C. Sander, "Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?" Protein Eng., vol. 7, pp. 349-358, 1994.
    • (1994) Protein Eng. , vol.7 , pp. 349-358
    • Shindyalov, I.N.1    Kolchanov, N.A.2    Sander, C.3
  • 15
    • 4043170491 scopus 로고    scopus 로고
    • Protein contact prediction using patterns of correlation
    • N. Hamilton, K. Burrage, M. A. Ragan, and T. Huber, "Protein contact prediction using patterns of correlation," Proteins, vol. 56, 679-684, 2004.
    • (2004) Proteins , vol.56 , pp. 679-684
    • Hamilton, N.1    Burrage, K.2    Ragan, M.A.3    Huber, T.4
  • 16
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: Novel prediction of long-range contacts
    • M. Punta and B. Rost, "PROFcon: Novel prediction of long-range contacts," Bioinformatics, vol. 21, pp. 2960-2968, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 17
    • 84876517773 scopus 로고    scopus 로고
    • CNNcon: Improved protein contact maps prediction using cascaded neural networks
    • W. Ding, J. Xie, D. Dai, H. Zhang, H. Xie, and W. Zhang, "CNNcon: Improved protein contact maps prediction using cascaded neural networks," PLoS One, vol. 8, p. e61533, 2013.
    • (2013) PLoS One , vol.8
    • Ding, W.1    Xie, J.2    Dai, D.3    Zhang, H.4    Xie, H.5    Zhang, W.6
  • 18
    • 84867316765 scopus 로고    scopus 로고
    • Deep architectures for protein contact map prediction
    • P. D. Lena, K. Nagata, and P. Baldi, "Deep architectures for protein contact map prediction," Bioinformatics, vol. 28, pp. 2449-2457, 2012.
    • (2012) Bioinformatics , vol.28 , pp. 2449-2457
    • Lena, P.D.1    Nagata, K.2    Baldi, P.3
  • 20
    • 84879987629 scopus 로고    scopus 로고
    • The role of balanced training and testing data sets for binary classifiers in bioinformatics
    • Q. Wei and R. L. Dunbrack Jr, "The role of balanced training and testing data sets for binary classifiers in bioinformatics," PLoS One, vol. 8, p. e67863, 2013.
    • (2013) PLoS One , vol.8
    • Wei, Q.1    Dunbrack, R.L.2
  • 23
    • 0030211964 scopus 로고    scopus 로고
    • Bagging predictors
    • L. Breiman, "Bagging predictors," Mach. Learn., vol. 24, pp. 123-140, 1996.
    • (1996) Mach. Learn. , vol.24 , pp. 123-140
    • Breiman, L.1
  • 24
    • 84950461478 scopus 로고
    • Estimating the error rate of a prediction rule: Improvement on cross-validation
    • B. Efron, "Estimating the error rate of a prediction rule: Improvement on cross-validation," J. Am. Stat. Assoc., vol. 78, pp. 316-331, 1983.
    • (1983) J. Am. Stat. Assoc. , vol.78 , pp. 316-331
    • Efron, B.1
  • 25
    • 84908542331 scopus 로고    scopus 로고
    • Combining physicochemical and evolutionary information for protein contact prediction
    • Oct
    • M. Schneider and O. Brock, "Combining physicochemical and evolutionary information for protein contact prediction," PLoS One, vol. 9, no. 10, Oct. 2014.
    • (2014) PLoS One , vol.9 , Issue.10
    • Schneider, M.1    Brock, O.2
  • 26
    • 84879976691 scopus 로고    scopus 로고
    • Predicting protein contact map using evolutionary and physical constraints by integer programming
    • Jul
    • Z. Wang and J. Xu, "Predicting protein contact map using evolutionary and physical constraints by integer programming," Bioinformatics, vol. 29, no. 13, pp. i266-i273, Jul. 2013.
    • (2013) Bioinformatics , vol.29 , Issue.13 , pp. i266-i273
    • Wang, Z.1    Xu, J.2
  • 27
    • 55549086519 scopus 로고    scopus 로고
    • Fragment-HMM: A new approach to protein structure prediction
    • S. C. Li, D. Bu, J. Xu, and M. Li, "Fragment-HMM: A new approach to protein structure prediction," Protein Sci., vol. 17, no. 11, pp. 1925-1934, 2008.
    • (2008) Protein Sci. , vol.17 , Issue.11 , pp. 1925-1934
    • Li, S.C.1    Bu, D.2    Xu, J.3    Li, M.4
  • 28
    • 77951941264 scopus 로고    scopus 로고
    • MULTICOM: A multi-level combination approach to protein structure prediction and its assessments in CASP8
    • Apr
    • Z. Wang, J. Eickholt, and J. Cheng, "MULTICOM: A multi-level combination approach to protein structure prediction and its assessments in CASP8," Bioinformatics, vol. 26, no. 7, pp. 882-888, Apr. 2010.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 882-888
    • Wang, Z.1    Eickholt, J.2    Cheng, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.