메뉴 건너뛰기




Volumn 2014, Issue , 2014, Pages

Protein binding site prediction by combining hidden markov support vector machine and profile-based propensities

Author keywords

[No Author keywords available]

Indexed keywords

ACCESSIBLE SURFACE AREA; ARTICLE; CORRELATION COEFFICIENT; HIDDEN MARKOV MODEL; MACHINE LEARNING; ORDER PROFILE PROPENSITY; POSITION SPECIFIC SCORE MATRIX; PREDICTION; PROTEIN BINDING; RANDOM FOREST; SEQUENCE ALIGNMENT; SUPPORT VECTOR MACHINE; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS;

EID: 84929056174     PISSN: 23566140     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1155/2014/464093     Document Type: Article
Times cited : (14)

References (45)
  • 1
    • 33846200437 scopus 로고    scopus 로고
    • Prediction-based fingerprints of protein-protein interactions
    • A. Porollo and J. Meller, "Prediction-based fingerprints of protein-protein interactions, " Proteins: Structure, Function and Genetics, vol. 66, no. 3, pp. 630-645, 2007.
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.3 , pp. 630-645
    • Porollo, A.1    Meller, J.2
  • 2
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • F. Glaser, D. M. Steinberg, I. A. Vakser, and N. Ben-Tal, "Residue frequencies and pairing preferences at protein-protein interfaces, " Proteins, vol. 43, no. 2, pp. 89-102, 2001.
    • (2001) Proteins , vol.43 , Issue.2 , pp. 89-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 3
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • W. L. DeLano, "Unraveling hot spots in binding interfaces: progress and challenges, " Current Opinion in Structural Biology, vol. 12, no. 1, pp. 14-20, 2002.
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.1 , pp. 14-20
    • DeLano, W.L.1
  • 4
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • H. Zhou and Y. Shan, "Prediction of protein interaction sites from sequence profile and residue neighbor list, " Proteins: Structure, Function and Genetics, vol. 44, no. 3, pp. 336-343, 2001.
    • (2001) Proteins: Structure, Function and Genetics , vol.44 , Issue.3 , pp. 336-343
    • Zhou, H.1    Shan, Y.2
  • 6
    • 24344484686 scopus 로고    scopus 로고
    • Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data
    • H. Chen and H. X. Zhou, "Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data, " Proteins: Structure, Function and Genetics, vol. 61, no. 1, pp. 21-35, 2005.
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.1 , pp. 21-35
    • Chen, H.1    Zhou, H.X.2
  • 7
    • 1842765629 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using support vector machines
    • A. Koike and T. Takagi, "Prediction of protein-protein interaction sites using support vector machines, " Protein Engineering, Design and Selection, vol. 17, no. 2, pp. 165-173, 2004.
    • (2004) Protein Engineering, Design and Selection , vol.17 , Issue.2 , pp. 165-173
    • Koike, A.1    Takagi, T.2
  • 8
    • 30644470508 scopus 로고    scopus 로고
    • Predicting protein interaction sites from residue spatial sequence profile and evolution rate
    • B. Wang, P. Chen, D. Huang, J. Li, T. Lok, and M. R. Lyu, "Predicting protein interaction sites from residue spatial sequence profile and evolution rate, " FEBS Letters, vol. 580, no. 2, pp. 380-384, 2006.
    • (2006) FEBS Letters , vol.580 , Issue.2 , pp. 380-384
    • Wang, B.1    Chen, P.2    Huang, D.3    Li, J.4    Lok, T.5    Lyu, M.R.6
  • 9
    • 33748779553 scopus 로고    scopus 로고
    • Insights into protein-protein Interfaces using a Bayesian network predictionmethod
    • J. R. Bradford, C. J. Needham, A. J. Bulpitt, and D. R. Westhead, "Insights into protein-protein Interfaces using a Bayesian network predictionmethod, " Journal ofMolecular Biology, vol. 362, no. 2, pp. 365-386, 2006.
    • (2006) Journal OfMolecular Biology , vol.362 , Issue.2 , pp. 365-386
    • Bradford, J.R.1    Needham, C.J.2    Bulpitt, A.J.3    Westhead, D.R.4
  • 10
    • 33751353420 scopus 로고    scopus 로고
    • Modelling interaction sites in protein domains with interaction profile hidden Markov models
    • T. Friedrich, B. Pils, T. Dandekar, J. Schultz, and T. Muller, "Modelling interaction sites in protein domains with interaction profile hidden Markov models, " Bioinformatics, vol. 22, no. 23, pp. 2851-2857, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.23 , pp. 2851-2857
    • Friedrich, T.1    Pils, B.2    Dandekar, T.3    Schultz, J.4    Muller, T.5
  • 11
    • 34548767667 scopus 로고    scopus 로고
    • Interaction-site prediction for protein complexes: A critical assessment
    • H. Zhou and S. Qin, "Interaction-site prediction for protein complexes: a critical assessment, " Bioinformatics, vol. 23, no. 17, pp. 2203-2209, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.17 , pp. 2203-2209
    • Zhou, H.1    Qin, S.2
  • 12
    • 68749110968 scopus 로고    scopus 로고
    • Exploitingthree kinds of interface propensities to identify protein binding sites
    • B. Liu, X. Wang, L. Lin, Q. Dong, and X. Wang, "Exploitingthree kinds of interface propensities to identify protein binding sites, " Computational Biology andChemistry, vol. 33, no. 4, pp. 303-311, 2009.
    • (2009) Computational Biology AndChemistry , vol.33 , Issue.4 , pp. 303-311
    • Liu, B.1    Wang, X.2    Lin, L.3    Dong, Q.4    Wang, X.5
  • 13
    • 71549172792 scopus 로고    scopus 로고
    • Prediction of protein binding sites in protein structures using hiddenMarkov support vector machine
    • article 381
    • B. Liu, X. Wang, L. Lin, B. Tang, and Q. Dong, "Prediction of protein binding sites in protein structures using hiddenMarkov support vector machine, " BMC Bioinformatics, vol. 10, article 381, 2009.
    • (2009) BMC Bioinformatics , vol.10
    • Liu, B.1    Wang, X.2    Lin, L.3    Tang, B.4    Dong, Q.5
  • 14
    • 33644873706 scopus 로고    scopus 로고
    • The RCSB PDB information portal for structural genomics
    • A. Kouranov, L. Xie, J. de la Cruz et al., "The RCSB PDB information portal for structural genomics, " Nucleic Acids Research., vol. 34, pp. D302-D305, 2006.
    • (2006) Nucleic Acids Research. , vol.34 , pp. D302-D305
    • Kouranov, A.1    Xie, L.2    De La Cruz, J.3
  • 17
    • 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. 22, no. 12, pp. 2577-2637, 1983.
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 18
    • 84867004398 scopus 로고    scopus 로고
    • Using amino acid physicochemical distance transformation for fast protein remote homology detection
    • Article ID e46633
    • B. Liu, X. Wang, Q. Chen, Q. Dong, and X. Lan, "Using amino acid physicochemical distance transformation for fast protein remote homology detection, " PLoS ONE, vol. 7, no. 9, Article ID e46633, 2012.
    • (2012) PLoS ONE , vol.7 , Issue.9
    • Liu, B.1    Wang, X.2    Chen, Q.3    Dong, Q.4    Lan, X.5
  • 19
    • 58149345703 scopus 로고    scopus 로고
    • A discriminativemethod for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis
    • article 510
    • B. Liu, X. Wang, L. Lin, and Q. Dong, "A discriminativemethod for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis, " BMC Bioinformatics, vol. 9, article 510, 2008.
    • (2008) BMC Bioinformatics , vol.9
    • Liu, B.1    Wang, X.2    Lin, L.3    Dong, Q.4
  • 20
    • 84892972298 scopus 로고    scopus 로고
    • Proteinremote homology detection by combining Chous pseudo amino acid composition and profile-based protein representation
    • B. Liu, X. Wang, Q. Zou, Q. Dong, and Q. Chen, "Proteinremote homology detection by combining Chous pseudo amino acid composition and profile-based protein representation, " Molecular Informatics, vol. 32, no. 9-10, pp. 775-782, 2013.
    • (2013) Molecular Informatics , vol.32 , Issue.9-10 , pp. 775-782
    • Liu, B.1    Wang, X.2    Zou, Q.3    Dong, Q.4    Chen, Q.5
  • 21
    • 84901288109 scopus 로고    scopus 로고
    • Using distances between Top-n-gram and residue pairs for protein remote homology detection
    • B. Liu, J. Xu, Q. Zou et al., "Using distances between Top-n-gram and residue pairs for protein remote homology detection, "BMC Bioinformatics, vol. 15, supplement 2, p. S3, 2014.
    • (2014) BMC Bioinformatics , vol.15 , pp. S3
    • Liu, B.1    Xu, J.2    Zou, Q.3
  • 22
    • 84892954329 scopus 로고    scopus 로고
    • Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection
    • B. Liu, "Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection, " Bioinformatics, vol. 30, no. 4, pp. 472-479, 2014.
    • (2014) Bioinformatics , vol.30 , Issue.4 , pp. 472-479
    • Liu, B.1
  • 23
    • 59149087824 scopus 로고    scopus 로고
    • Prediction of proteinprotein interaction sites in sequences and 3D structures by
    • random forests Article ID e1000278
    • M. Sikic, S. Tomic, and K. Vlahoviɥek, "Prediction of proteinprotein interaction sites in sequences and 3D structures by random forests, " PLoS Computational Biology, vol. 5, no. 1, Article ID e1000278, 2009.
    • (2009) PLoS Computational Biology , vol.5 , Issue.1
    • Sikic, M.1    Tomic, S.2    Vlahoviɥek, K.3
  • 24
    • 34047104592 scopus 로고    scopus 로고
    • Protein-protein interaction site prediction based on conditional random fields
    • M. H. Li, L. Lin, X. Wang, and T. Liu, "Protein-protein interaction site prediction based on conditional random fields, " Bioinformatics, vol. 23, no. 5, pp. 597-604, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 597-604
    • Li, M.H.1    Lin, L.2    Wang, X.3    Liu, T.4
  • 25
    • 84887196363 scopus 로고    scopus 로고
    • QChIPat: A quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions
    • B. Liu, "QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions, " BMC Genomics, vol. 14, supplement 8, p. S3, 2013.
    • (2013) BMC Genomics , vol.14 , pp. S3
    • Liu, B.1
  • 26
    • 84863432335 scopus 로고    scopus 로고
    • Prediction of ketoacyl synthase family using reduced amino acid alphabets
    • W. Chen, P. Feng, and H. Lin, "Prediction of ketoacyl synthase family using reduced amino acid alphabets, " Journal of IndustrialMicrobiology and Biotechnology, vol. 39, no. 4, pp. 579-584, 2012.
    • (2012) Journal of IndustrialMicrobiology and Biotechnology , vol.39 , Issue.4 , pp. 579-584
    • Chen, W.1    Feng, P.2    Lin, H.3
  • 27
    • 84885112194 scopus 로고    scopus 로고
    • AcalPred: A sequence-based tool for discriminating between acidic and alkaline enzymes
    • Article IDe75726
    • H. Lin, W. Chen, and H. Ding, "AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes, " PLoS ONE, vol. 8, no. 10, Article IDe75726, 2013.
    • (2013) PLoS ONE , vol.8 , Issue.10
    • Lin, H.1    Chen, W.2    Ding, H.3
  • 28
    • 84898434605 scopus 로고    scopus 로고
    • DNA physical parameters modulate nucleosome positioning in the Saccharomyces cerevisiae genome
    • W. Chen, H. Lin, and P. M. Feng, "DNA physical parameters modulate nucleosome positioning in the Saccharomyces cerevisiae genome, " Current Bioinformatics, vol. 9, no. 2, pp. 188-193, 2014.
    • (2014) Current Bioinformatics , vol.9 , Issue.2 , pp. 188-193
    • Chen, W.1    Lin, H.2    Feng, P.M.3
  • 29
    • 84884269845 scopus 로고    scopus 로고
    • Identification of antioxidants from sequence information using Naive Bayes
    • Article ID 567529
    • P.-M. Feng, H. Lin, and W. Chen, "Identification of antioxidants from sequence information using Naive Bayes, " Computational and Mathematical Methods in Medicine, vol. 2013, Article ID 567529, 5 pages, 2013.
    • (2013) Computational and Mathematical Methods in Medicine , vol.2013 , pp. 5
    • Feng, P.-M.1    Lin, H.2    Chen, W.3
  • 30
    • 84870391329 scopus 로고    scopus 로고
    • Identification ofmycobacterialmembrane proteins and their types using overrepresented tripeptide compositions
    • C. Ding, L. Yuan, S. Guo, H. Lin, and W. Chen, "Identification ofmycobacterialmembrane proteins and their types using overrepresented tripeptide compositions, " Journal of Proteomics, vol. 77, pp. 321-328, 2012.
    • (2012) Journal of Proteomics , vol.77 , pp. 321-328
    • Ding, C.1    Yuan, L.2    Guo, S.3    Lin, H.4    Chen, W.5
  • 31
    • 84862831800 scopus 로고    scopus 로고
    • Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine
    • W. Chen and H. Lin, "Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine, " Computers in Biology andMedicine, vol. 42, no. 4, pp. 504-507, 2012.
    • (2012) Computers in Biology AndMedicine , vol.42 , Issue.4 , pp. 504-507
    • Chen, W.1    Lin, H.2
  • 32
    • 84885640993 scopus 로고    scopus 로고
    • IHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
    • P. M. Feng, W. Chen, H. Lin, and K. Chou, "iHSP-PseRAAAC: identifying the heat shock protein families using pseudo reduced amino acid alphabet composition, "Analytical Biochemistry, vol. 442, no. 1, pp. 118-125, 2013.
    • (2013) Analytical Biochemistry , vol.442 , Issue.1 , pp. 118-125
    • Feng, P.M.1    Chen, W.2    Lin, H.3    Chou, K.4
  • 33
    • 84868128310 scopus 로고    scopus 로고
    • INuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties
    • Article ID e47843
    • W. Chen, H. Lin, P. Feng, C. Ding, Y. Zuo, and K. Chou, "iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties, " PLoS ONE, vol. 7, no. 10, Article ID e47843, 2012.
    • (2012) PLoS ONE , vol.7 , Issue.10
    • Chen, W.1    Lin, H.2    Feng, P.3    Ding, C.4    Zuo, Y.5    Chou, K.6
  • 34
    • 84896463976 scopus 로고    scopus 로고
    • INuc-PseKNC: A sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    • S. H. Guo, E. Z. Deng, L. Q. Xu et al., "iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition, " Bioinformatics, vol. 30, no. 11, pp. 1522-1529, 2014.
    • (2014) Bioinformatics , vol.30 , Issue.11 , pp. 1522-1529
    • Guo, S.H.1    Deng, E.Z.2    Xu, L.Q.3
  • 35
    • 84876053736 scopus 로고    scopus 로고
    • IRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition
    • W. Chen, P. Feng, H. Lin, and K. Chou, "IRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition, " Nucleic Acids Research, vol. 41, no. 6, p. e68, 2013.
    • (2013) Nucleic Acids Research , vol.41 , Issue.6 , pp. e68
    • Chen, W.1    Feng, P.2    Lin, H.3    Chou, K.4
  • 36
    • 84878657414 scopus 로고    scopus 로고
    • Naive bayes classifier with feature selection to identify phage virion proteins
    • Article ID 530696
    • P. Feng, H. Ding, W. Chen, and H. Lin, "Naive bayes classifier with feature selection to identify phage virion proteins, " Computational and Mathematical Methods in Medicine, vol. 2013, Article ID 530696, 6 pages, 2013.
    • (2013) Computational and Mathematical Methods in Medicine , vol.2013 , pp. 6
    • Feng, P.1    Ding, H.2    Chen, W.3    Lin, H.4
  • 37
    • 84876306464 scopus 로고    scopus 로고
    • Prediction of Golgi-resident protein types by using feature selection technique
    • H. Ding, S. Guo, E. Deng et al., "Prediction of Golgi-resident protein types by using feature selection technique, " Chemometrics and Intelligent Laboratory Systems, vol. 124, pp. 9-13, 2013.
    • (2013) Chemometrics and Intelligent Laboratory Systems , vol.124 , pp. 9-13
    • Ding, H.1    Guo, S.2    Deng, E.3
  • 38
    • 77958151520 scopus 로고    scopus 로고
    • Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information
    • W. Chen and H. Lin, "Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information, " Biochemical and Biophysical Research Communications, vol. 401, no. 3, pp. 382-384, 2010.
    • (2010) Biochemical and Biophysical Research Communications , vol.401 , Issue.3 , pp. 382-384
    • Chen, W.1    Lin, H.2
  • 39
    • 78650178724 scopus 로고    scopus 로고
    • Prediction of subcellular location of mycobacterial protein using feature selection techniques
    • H. Lin, H. Ding, F. Guo, and J. Huang, "Prediction of subcellular location of mycobacterial protein using feature selection techniques, " Molecular Diversity, vol. 14, no. 4, pp. 667-671, 2010.
    • (2010) Molecular Diversity , vol.14 , Issue.4 , pp. 667-671
    • Lin, H.1    Ding, H.2    Guo, F.3    Huang, J.4
  • 40
    • 78650209947 scopus 로고    scopus 로고
    • Prediction of thermophilic proteins using feature selection technique
    • H. Lin and W. Chen, "Prediction of thermophilic proteins using feature selection technique, " Journal ofMicrobiologicalMethods, vol. 84, no. 1, pp. 67-70, 2011.
    • (2011) Journal OfMicrobiologicalMethods , vol.84 , Issue.1 , pp. 67-70
    • Lin, H.1    Chen, W.2
  • 41
    • 84900463301 scopus 로고    scopus 로고
    • PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
    • W. Chen, T. Y. Lei, D. C. Jin, H. Lin, and K. C. Chou, "PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition, " Analytical Biochemistry, vol. 456, pp. 53-60, 2014.
    • (2014) Analytical Biochemistry , vol.456 , pp. 53-60
    • Chen, W.1    Lei, T.Y.2    Jin, D.C.3    Lin, H.4    Chou, K.C.5
  • 42
    • 84878789801 scopus 로고    scopus 로고
    • Using overrepresented tetrapeptides to predict protein submitochondria locations
    • H. Lin, W. Chen, L. Yuan, Z. Li, and H. Ding, "Using overrepresented tetrapeptides to predict protein submitochondria locations, " Acta Biotheoretica, vol. 61, no. 2, pp. 259-268, 2013.
    • (2013) Acta Biotheoretica , vol.61 , Issue.2 , pp. 259-268
    • Lin, H.1    Chen, W.2    Yuan, L.3    Li, Z.4    Ding, H.5
  • 44
    • 84881519843 scopus 로고    scopus 로고
    • Binmempredict: A web server and software for predicting membrane protein types
    • Q. Zou, X. Li, Y. Jiang, Y. Zhao, and G. Wang, "Binmempredict: a web server and software for predicting membrane protein types, " Current Proteomics, vol. 10, no. 1, pp. 2-9, 2013.
    • (2013) Current Proteomics , vol.10 , Issue.1 , pp. 2-9
    • Zou, Q.1    Li, X.2    Jiang, Y.3    Zhao, Y.4    Wang, G.5
  • 45
    • 84874240374 scopus 로고    scopus 로고
    • Hierarchical classification of protein folds using a novel ensemble classifier
    • Article ID e56499
    • C. Lin, Y. Zou, J. Qin et al., "Hierarchical classification of protein folds using a novel ensemble classifier, " PLoS ONE, vol. 8, no. 2, Article ID e56499, 2013.
    • (2013) PLoS ONE , vol.8 , Issue.2
    • Lin, C.1    Zou, Y.2    Qin, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.