메뉴 건너뛰기




Volumn 353, Issue 1, 2007, Pages 164-169

Using amino acid and peptide composition to predict membrane protein types

Author keywords

GPI anchored membrane protein; Lipid chain anchored membrane protein; Multipass transmembrane protein; The stepwise discriminant analysis; Type I membrane protein; Type II membrane protein

Indexed keywords

MEMBRANE PROTEIN;

EID: 33845733642     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.12.004     Document Type: Article
Times cited : (34)

References (31)
  • 3
    • 20544463153 scopus 로고    scopus 로고
    • Structure and inter-domain interactions of domain II from the blood-stage malarial protein, apical membrane antigen 1
    • Feng Z.P., Keizer D.W., Stevenson R.A., Yao S., Babon J.J., Murphy V.J., Anders R.F., and Norton R.S. Structure and inter-domain interactions of domain II from the blood-stage malarial protein, apical membrane antigen 1. J. Mol. Biol. 350 (2005) 641-656
    • (2005) J. Mol. Biol. , vol.350 , pp. 641-656
    • Feng, Z.P.1    Keizer, D.W.2    Stevenson, R.A.3    Yao, S.4    Babon, J.J.5    Murphy, V.J.6    Anders, R.F.7    Norton, R.S.8
  • 4
    • 33750711671 scopus 로고    scopus 로고
    • Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes
    • Feng Z.P., Zhang X., Han P., Arora N., Anders R.F., and Norton R.S. Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes. Mol. Biochem. Parasitol. 150 (2006) 256-267
    • (2006) Mol. Biochem. Parasitol. , vol.150 , pp. 256-267
    • Feng, Z.P.1    Zhang, X.2    Han, P.3    Arora, N.4    Anders, R.F.5    Norton, R.S.6
  • 5
    • 33745630355 scopus 로고    scopus 로고
    • A set of glycosylphosphatidyl inositol-anchored membrane proteins of Plasmodium falciparum is refractory to genetic deletion
    • Sanders P.R., Kats L.M., Drew D.R., O'Donnell R.A., O'Neill M., Maier A.G., Coppel R.L., and Crabb B.S. A set of glycosylphosphatidyl inositol-anchored membrane proteins of Plasmodium falciparum is refractory to genetic deletion. Infect. Immun. 74 (2006) 4330-4338
    • (2006) Infect. Immun. , vol.74 , pp. 4330-4338
    • Sanders, P.R.1    Kats, L.M.2    Drew, D.R.3    O'Donnell, R.A.4    O'Neill, M.5    Maier, A.G.6    Coppel, R.L.7    Crabb, B.S.8
  • 6
    • 0034844091 scopus 로고    scopus 로고
    • Trafficking and localisation of resident Golgi glycosylation enzymes
    • Opat A.S., van Vliet C., and Gleeson P.A. Trafficking and localisation of resident Golgi glycosylation enzymes. Biochimie 83 (2001) 63-773
    • (2001) Biochimie , vol.83 , pp. 63-773
    • Opat, A.S.1    van Vliet, C.2    Gleeson, P.A.3
  • 8
    • 33750266831 scopus 로고    scopus 로고
    • Trafficking and signaling by fatty-acylated and prenylated proteins
    • Resh M.D. Trafficking and signaling by fatty-acylated and prenylated proteins. Nat. Chem. Biol. 2 (2006) 584-590
    • (2006) Nat. Chem. Biol. , vol.2 , pp. 584-590
    • Resh, M.D.1
  • 9
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 10
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: application to topology prediction
    • Tusnady G.E., and Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283 (1998) 489-506
    • (1998) J. Mol. Biol. , vol.283 , pp. 489-506
    • Tusnady, G.E.1    Simon, I.2
  • 11
    • 0033600935 scopus 로고    scopus 로고
    • Prediction of potential GPI-modification sites in proprotein sequences
    • Eisenhaber B., Bork P., and Eisenhaber F. Prediction of potential GPI-modification sites in proprotein sequences. J. Mol. Biol. 292 (1999) 741-758
    • (1999) J. Mol. Biol. , vol.292 , pp. 741-758
    • Eisenhaber, B.1    Bork, P.2    Eisenhaber, F.3
  • 12
    • 33748449804 scopus 로고    scopus 로고
    • Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition
    • Wang S.Q., Yang J., and Chou K.C. Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition. J. Theor. Biol. 242 (2006) 941-946
    • (2006) J. Theor. Biol. , vol.242 , pp. 941-946
    • Wang, S.Q.1    Yang, J.2    Chou, K.C.3
  • 13
    • 28444431990 scopus 로고    scopus 로고
    • Using fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types
    • Liu H., Yang J., Wang M., Xue L., and Chou K.C. Using fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types. Protein J. 24 (2005) 385-389
    • (2005) Protein J. , vol.24 , pp. 385-389
    • Liu, H.1    Yang, J.2    Wang, M.3    Xue, L.4    Chou, K.C.5
  • 14
    • 33748150984 scopus 로고    scopus 로고
    • Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition
    • Shen H.B., Yang J., and Chou K.C. Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition. J. Theor. Biol. 240 (2006) 9-13
    • (2006) J. Theor. Biol. , vol.240 , pp. 9-13
    • Shen, H.B.1    Yang, J.2    Chou, K.C.3
  • 15
    • 25144470285 scopus 로고    scopus 로고
    • Low-frequency Fourier spectrum for predicting membrane protein types
    • Liu H., Wang M., and Chou K.C. Low-frequency Fourier spectrum for predicting membrane protein types. Biochem. Biophys. Res. Commun. 336 (2005) 737-739
    • (2005) Biochem. Biophys. Res. Commun. , vol.336 , pp. 737-739
    • Liu, H.1    Wang, M.2    Chou, K.C.3
  • 16
    • 22144487766 scopus 로고    scopus 로고
    • Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types
    • Shen H., and Chou K.C. Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types. Biochem. Biophys. Res. Commun. 334 (2005) 288-292
    • (2005) Biochem. Biophys. Res. Commun. , vol.334 , pp. 288-292
    • Shen, H.1    Chou, K.C.2
  • 17
    • 18344391868 scopus 로고    scopus 로고
    • Prediction of membrane protein types by incorporating amphipathic effects
    • Chou K.C., and Cai Y.D. Prediction of membrane protein types by incorporating amphipathic effects. J. Chem. Inf. Model. 45 (2005) 407-413
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 407-413
    • Chou, K.C.1    Cai, Y.D.2
  • 18
    • 11844306688 scopus 로고    scopus 로고
    • Using GO-PseAA predictor to identify membrane proteins and their types
    • Chou K.C., and Cai Y.D. Using GO-PseAA predictor to identify membrane proteins and their types. Biochem. Biophys. Res. Commun. 327 (2005) 845-847
    • (2005) Biochem. Biophys. Res. Commun. , vol.327 , pp. 845-847
    • Chou, K.C.1    Cai, Y.D.2
  • 19
    • 6344231856 scopus 로고    scopus 로고
    • SLLE for predicting membrane protein types
    • Wang M., Yang J., Xu Z.J., and Chou K.C. SLLE for predicting membrane protein types. J. Theor. Biol. 232 (2005) 7-15
    • (2005) J. Theor. Biol. , vol.232 , pp. 7-15
    • Wang, M.1    Yang, J.2    Xu, Z.J.3    Chou, K.C.4
  • 20
    • 8444248846 scopus 로고    scopus 로고
    • Weighted-support vector machines for predicting membrane protein types based on pseudo-amino acid composition
    • Wang M., Yang J., Liu G.P., Xu Z.J., and Chou K.C. Weighted-support vector machines for predicting membrane protein types based on pseudo-amino acid composition. Protein Eng. Des. Sel. 17 (2004) 509-516
    • (2004) Protein Eng. Des. Sel. , vol.17 , pp. 509-516
    • Wang, M.1    Yang, J.2    Liu, G.P.3    Xu, Z.J.4    Chou, K.C.5
  • 21
    • 0036805375 scopus 로고    scopus 로고
    • Predicting membrane protein types using residue-pair models based on reduced similarity dataset
    • Yang X.G., and Feng Z.P. Predicting membrane protein types using residue-pair models based on reduced similarity dataset. J. Biomol. Struct. Dyn. 20 (2002) 163-172
    • (2002) J. Biomol. Struct. Dyn. , vol.20 , pp. 163-172
    • Yang, X.G.1    Feng, Z.P.2
  • 22
    • 0033781978 scopus 로고    scopus 로고
    • Prediction of membrane protein types based on the hydrophobic index of amino acids
    • Feng Z.P., and Zhang C.T. Prediction of membrane protein types based on the hydrophobic index of amino acids. J. Protein Chem. 19 (2000) 269-275
    • (2000) J. Protein Chem. , vol.19 , pp. 269-275
    • Feng, Z.P.1    Zhang, C.T.2
  • 23
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch A., and Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28 (2000) 45-48
    • (2000) Nucleic Acids Res. , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 24
    • 0036169928 scopus 로고    scopus 로고
    • Tolerating some redundancy significantly speeds up clustering of large protein databases
    • Li W., Jaroszewski L., and Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18 (2002) 77-82
    • (2002) Bioinformatics , vol.18 , pp. 77-82
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 25
    • 0000012036 scopus 로고
    • Comparison of stopping rules in forward stepwise discriminant analysis
    • Costanza M.C., and Afifi A.A. Comparison of stopping rules in forward stepwise discriminant analysis. J. Am. Stat. Asso. 74 (1979) 777-785
    • (1979) J. Am. Stat. Asso. , vol.74 , pp. 777-785
    • Costanza, M.C.1    Afifi, A.A.2
  • 26
    • 0036051172 scopus 로고    scopus 로고
    • Prediction of protein structural class by amino acid and polypeptide composition
    • Luo R.Y., Feng Z.P., and Liu J.K. Prediction of protein structural class by amino acid and polypeptide composition. Eur. J. Biochem. 269 (2002) 4219-4225
    • (2002) Eur. J. Biochem. , vol.269 , pp. 4219-4225
    • Luo, R.Y.1    Feng, Z.P.2    Liu, J.K.3
  • 27
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • Baldi P., Brunak S., Chauvin Y., Andersen C.A.F., and Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16 (2000) 412-424
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.F.4    Nielsen, H.5
  • 29
    • 0022631926 scopus 로고
    • The folding type of a protein is relevant to the amino acid composition
    • Nakashima H., Nishikawa K., and Ooi T. The folding type of a protein is relevant to the amino acid composition. J. Biochem. 99 (1986) 152-162
    • (1986) J. Biochem. , vol.99 , pp. 152-162
    • Nakashima, H.1    Nishikawa, K.2    Ooi, T.3
  • 30
    • 0031588694 scopus 로고    scopus 로고
    • Relation between amino acid composition and cellular location of proteins
    • Cedano J., Aloy P., P_erez-Pons J.A., and Querol E. Relation between amino acid composition and cellular location of proteins. J. Mol. Biol. 266 (1997) 594-600
    • (1997) J. Mol. Biol. , vol.266 , pp. 594-600
    • Cedano, J.1    Aloy, P.2    Perez-Pons, J.A.3    Querol, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.