메뉴 건너뛰기




Volumn 78, Issue 7, 2010, Pages 1789-1797

Classification of transporters using efficient radial basis function networks with position - Specific scoring matrices and biochemical properties

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID COMPOSITION; ARTICLE; CHEMICAL ANALYSIS; ELECTROCHEMICAL ANALYSIS; ESCHERICHIA COLI; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PSEUDOMONAS AERUGINOSA; SCORING SYSTEM;

EID: 77951225212     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22694     Document Type: Article
Times cited : (55)

References (29)
  • 1
    • 33846040629 scopus 로고    scopus 로고
    • TransportDB: A comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
    • Ren QH, Chen KX, Paulsen IT. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 2007;35:D274D279.
    • (2007) Nucleic Acids Res , vol.35
    • Ren, Q.H.1    Chen, K.X.2    Paulsen, I.T.3
  • 2
    • 0343603660 scopus 로고    scopus 로고
    • A functional-phylogenetic classification system for transmembrane solute transporters
    • Saier MH. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 2000;64: 354-411,
    • (2000) Microbiol Mol Biol Rev , vol.64 , pp. 354-411
    • Saier, M.H.1
  • 3
    • 33644873454 scopus 로고    scopus 로고
    • TCDB: The transporter classification database for membrane transport protein analyses and information
    • Saier MH, Tran CV, Barabote RD. TCDB: the transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res 2006;34:D181-D186.
    • (2006) Nucleic Acids Res , vol.34
    • Saier, M.H.1    Tran, C.V.2    Barabote, R.D.3
  • 4
    • 0031826040 scopus 로고    scopus 로고
    • SOSUI: Classification and secondary structure prediction system for membrane proteins
    • Hirokawa T, Boon-Chieng S, Mltaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998:14:378-379.
    • (1998) Bioinformatics , vol.14 , pp. 378-379
    • Hirokawa, T.1    Boon-Chieng, S.2    Mltaku, S.3
  • 5
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnady GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics 2001;17:849-850.
    • (2001) Bioinformatics , vol.17 , pp. 849-850
    • Tusnady, G.E.1    Simon, I.2
  • 6
    • 16344376554 scopus 로고    scopus 로고
    • A simple statistical method for discriminating outer membrane proteins with better accuracy
    • Gromiha MM, Suwa M. A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics 2005;21:961-968.
    • (2005) Bioinformatics , vol.21 , pp. 961-968
    • Gromiha, M.M.1    Suwa, M.2
  • 7
    • 29244482784 scopus 로고    scopus 로고
    • Predicting membrane protein type by functional domain composition and pseudo-ami.no acid composition
    • Cai YD, Chou KC. Predicting membrane protein type by functional domain composition and pseudo-ami.no acid composition. J Theor Biol 2006;238:395-400.
    • (2006) J Theor Biol , vol.238 , pp. 395-400
    • Cai, Y.D.1    Chou, K.C.2
  • 8
    • 2942522711 scopus 로고    scopus 로고
    • A Hidden Markov model method, capable of predicting and discriminating beta-barrel outer membrane proteins
    • Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. A Hidden Markov model method, capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics 2004;5.
    • (2004) BMC Bioinformatics , vol.5
    • Bagos, P.G.1    Liakopoulos, T.D.2    Spyropoulos, I.C.3    Hamodrakas, S.J.4
  • 9
    • 2642587355 scopus 로고    scopus 로고
    • Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods
    • Natt NK, Kaur H, Raghava. GPS. Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. Proteins: Struct Funct Bioinform 2004;56:11-18.
    • (2004) Proteins: Struct Funct Bioinform , vol.56 , pp. 11-18
    • Natt, N.K.1    Kaur, H.2    Raghava, G.P.S.3
  • 10
    • 33646780174 scopus 로고    scopus 로고
    • Discrimination of outer membrane proteins using machine learning algorithms
    • Gromiha MM, Suwa M. Discrimination of outer membrane proteins using machine learning algorithms. Proteins: Struct Funct Bioinform. 2006;63:1031-1037.
    • (2006) Proteins: Struct Funct Bioinform , vol.63 , pp. 1031-1037
    • Gromiha, M.M.1    Suwa, M.2
  • 11
    • 33748489925 scopus 로고    scopus 로고
    • Influence of amino acid properties for discriminating outer membrane proteins at better accuracy
    • Gromiha MM, Suwa M. Influence of amino acid properties for discriminating outer membrane proteins at better accuracy. Biochim Biophys Acta 2006;1764:1493-1497.
    • (2006) Biochim Biophys Acta , vol.1764 , pp. 1493-1497
    • Gromiha, M.M.1    Suwa, M.2
  • 12
    • 4243671284 scopus 로고    scopus 로고
    • A sequence-profilebased HMM for predicting and discriminating beta barrel membrane proteins
    • Martelli PL, Fariselli P, Krogh A, Casadio R. A sequence-profilebased HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 2002;18(Suppl l):46-53.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. L , pp. 46-53
    • Martelli, P.L.1    Fariselli, P.2    Krogh, A.3    Casadio, R.4
  • 13
    • 41049110433 scopus 로고    scopus 로고
    • Functional discrimination of membrane proteins using machine learning techniques
    • Gromiha MM, Yabuki Y. Functional discrimination of membrane proteins using machine learning techniques. BMC Bioinformatics 2008;9.
    • (2008) BMC Bioinformatics , vol.9
    • Gromiha, M.M.1    Yabuki, Y.2
  • 14
    • 42649092537 scopus 로고    scopus 로고
    • A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
    • Li HQ, Dai XB, Zhao XC. A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. Bioinformatics 2008;24:1129-1136.
    • (2008) Bioinformatics , vol.24 , pp. 1129-1136
    • Li, H.Q.1    Dai, X.B.2    Zhao, X.C.3
  • 17
    • 13844272392 scopus 로고    scopus 로고
    • Bio-basis function neural network for prediction of protease cleavage sites in proteins
    • Yang ZR, Thomson R. Bio-basis function neural network for prediction of protease cleavage sites in proteins. IEEE Trans Neural Networks 2005;16:263-274.
    • (2005) IEEE Trans Neural Networks , vol.16 , pp. 263-274
    • Yang, Z.R.1    Thomson, R.2
  • 18
    • 22144489879 scopus 로고    scopus 로고
    • Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme
    • Zhang GZ, Huang DS. Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. J Computer-Aided Mol Des 2004;18:797-810.
    • (2004) J Computer-Aided Mol des , vol.18 , pp. 797-810
    • Zhang, G.Z.1    Huang, D.S.2
  • 19
    • 33746952996 scopus 로고    scopus 로고
    • Protein, disorder prediction by condensed PSSM. considering propensity for order or disorder
    • Su CT, Chen CY, Ou YY. Protein, disorder prediction by condensed PSSM. considering propensity for order or disorder. BMC Bioinformatics 2006;7.
    • (2006) BMC Bioinformatics , vol.7
    • Su, C.T.1    Chen, C.Y.2    Ou, Y.Y.3
  • 20
    • 43249097732 scopus 로고    scopus 로고
    • Tmbetadisc-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles
    • Ou YY, Gromiha MM, Chen. SA, Suwa M. TMBETADISC-RBF: discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comput Biol Chem 2008;32:227-231.
    • (2008) Comput Biol Chem , vol.32 , pp. 227-231
    • Ou, Y.Y.1    Gromiha, M.M.2    Chen, S.A.3    Suwa, M.4
  • 21
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT Protein secondary structure prediction based on position-specific scoring matrices. J MoI Biol 1999;292:195-202.
    • (1999) J MoI Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 22
    • 23144461988 scopus 로고    scopus 로고
    • Locsvmpsi: A web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST
    • Xie D, Li A, Wang MH, Fan ZW, Feng HQ. LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids Res 2005,;33:W105-W110.
    • (2005) Nucleic Acids Res , vol.33
    • Xie, D.1    Li, A.2    Wang, M.H.3    Fan, Z.W.4    Feng, H.Q.5
  • 23
    • 0032979568 scopus 로고    scopus 로고
    • Importance of long-range interactions in protein folding
    • Gromiha MM, Selvaraj S. Importance of long-range interactions in protein folding. Biophys Chem 1999;77:49-68.
    • (1999) Biophys Chem , vol.77 , pp. 49-68
    • Gromiha, M.M.1    Selvaraj, S.2
  • 24
    • 33747822326 scopus 로고    scopus 로고
    • Fold-rate: Prediction of protein folding rates from amino acid sequence
    • Gromiha. MM, Thangakani AM, Selvaraj S. FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Res 2006;34:W70-W74.
    • (2006) Nucleic Acids Res , vol.34
    • Gromiha, M.M.1    Thangakani, A.M.2    Selvaraj, S.3
  • 25
    • 18344371857 scopus 로고    scopus 로고
    • A statistical model for predicting protein folding rates from amino acid sequence with structural class information
    • Gromiha MM. A statistical model for predicting protein folding rates from amino acid sequence with structural class information. J Chem Inf Model 2005;45:494-501.
    • (2005) J Chem Inf Model , vol.45 , pp. 494-501
    • Gromiha, M.M.1
  • 26
    • 71749092366 scopus 로고    scopus 로고
    • Combining SVMs with various feature selection strategies
    • Vancouver
    • Lin C-J, Chen Y-W. Combining SVMs with various feature selection strategies. In: NIPS 2003 Feature Selection Challenge, Vancouver 2003. pp 1-10.
    • (2003) NIPS 2003 Feature Selection Challenge , pp. 1-10
    • Lin, C.-J.1    Chen, Y.-W.2
  • 28
    • 3242879514 scopus 로고    scopus 로고
    • Bomp: A program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
    • Berven FS, Flikka K, Jensen HB, Eidhammer I, BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Nucleic Acids Res 2004; 32:W394-W399.
    • (2004) Nucleic Acids Res , vol.32
    • Berven, F.S.1    Flikka, K.2    Jensen, H.B.3    Eidhammer, I.4
  • 29
    • 33747846585 scopus 로고    scopus 로고
    • ProFtmb: A web server for predicting bacterial transmembrane beta barrel proteins
    • Bigelow H, Rost B. PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res 2006;34: W186-W188.
    • (2006) Nucleic Acids Res , vol.34
    • Bigelow, H.1    Rost, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.