메뉴 건너뛰기




Volumn 31, Issue 1, 2003, Pages 406-409

TMPDB: A database of experimentally-characterized transmembrane topoligies

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE LINKED OLIGOSACCHARIDE; CYSTEINE; MEMBRANE PROTEIN;

EID: 0037249645     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg020     Document Type: Review
Times cited : (90)

References (33)
  • 1
    • 0034213573 scopus 로고    scopus 로고
    • Do more complex organisms have a greater proportion of membrane proteins in their genomes?
    • Stevens,T.J. and Arkin,I.T. (2000) Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins, 39, 417-420.
    • (2000) Proteins , vol.39 , pp. 417-420
    • Stevens, T.J.1    Arkin, I.T.2
  • 2
    • 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. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 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
  • 3
    • 0034808117 scopus 로고    scopus 로고
    • Comparing function and structure between entire proteomes
    • Liu,J. and Rost,B. (2001) Comparing function and structure between entire proteomes. Protein Sci., 10, 1970-1979.
    • (2001) Protein Sci. , vol.10 , pp. 1970-1979
    • Liu, J.1    Rost, B.2
  • 4
    • 0012882896 scopus 로고    scopus 로고
    • Comprehensive analysis of transmembrane protein sequences in 39 microbial genomes
    • Matsuda,H., Wong,L., Miyano,S. and Takagi,T. (eds), Universal Academy Press, Tokyo
    • Arai,M., Noto,K., Lao,D.M., Ikeda,M. and Shimizu,T. (2001) Comprehensive analysis of transmembrane protein sequences in 39 microbial genomes. In Matsuda,H., Wong,L., Miyano,S. and Takagi,T. (eds), Genome Informatics 2001. Universal Academy Press, Tokyo, pp. 338-339.
    • (2001) Genome Informatics 2001 , pp. 338-339
    • Arai, M.1    Noto, K.2    Lao, D.M.3    Ikeda, M.4    Shimizu, T.5
  • 6
    • 0012771928 scopus 로고    scopus 로고
    • Comprehensive functional identification of prokaryotic transmembrane proteins by binary topology pattern
    • Matsuda,H., Wong,L., Miyano,S. and Takagi,T. (eds), Universal Academy Press, Tokyo
    • Sugiyama,Y., Arai,M. and Shimizu,T. (2001) Comprehensive functional identification of prokaryotic transmembrane proteins by binary topology pattern. In Matsuda,H., Wong,L., Miyano,S. and Takagi,T. (eds), Genome Informatics 2001. Universal Academy Press, Tokyo, pp. 334-335.
    • (2001) Genome Informatics 2001 , pp. 334-335
    • Sugiyama, Y.1    Arai, M.2    Shimizu, T.3
  • 7
    • 0021847027 scopus 로고
    • The detection and classification of membrane-spanning proteins
    • Klein,P., Kanehisa,M. and De Lisi,C. (1985) The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta, 815, 468-476.
    • (1985) Biochim. Biophys. Acta , vol.815 , pp. 468-476
    • Klein, P.1    Kanehisa, M.2    De Lisi, C.3
  • 8
    • 0000207681 scopus 로고
    • TMbase-a database of membrane spanning proteins segments
    • Hofmann,K. and Stoffel,W. (1993) TMbase-a database of membrane spanning proteins segments. Biol. Chem. Hoppe Seyler, 347, 166.
    • (1993) Biol. Chem. Hoppe Seyler , vol.347 , pp. 166
    • Hofmann, K.1    Stoffel, W.2
  • 9
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones,D.T., Taylor,W.R. and Thornton,J.M. (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 33, 3038-3049.
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 10
    • 0028568176 scopus 로고
    • TopPred II: An improved software for membrane protein structure predictions
    • Claros,M.G. and von Heijne,G. (1994) TopPred II: An improved software for membrane protein structure predictions. Comput. Appl. Biosci., 10, 685-686.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 685-686
    • Claros, M.G.1    von Heijne, G.2
  • 11
    • 0029978247 scopus 로고    scopus 로고
    • HTP: A neural network-based method for predicting the topology of helical transmembrane domains in proteins
    • Fariselli,P. and Casadio,R. (1996) HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. Comput. Appl. Biosci., 12, 41-48.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 41-48
    • Fariselli, P.1    Casadio, R.2
  • 12
    • 0030347515 scopus 로고    scopus 로고
    • Refining neural network predictions for helical transmembrane proteins by dynamic programming
    • States,D.T., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R.F. (eds), AAAI Press, Menlo Park, California
    • Rost,B., Casadio,R. and Fariselli,P. (1996) Refining neural network predictions for helical transmembrane proteins by dynamic programming. In States,D.T., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R.F. (eds), Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, California, pp. 192-200.
    • (1996) Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology , pp. 192-200
    • Rost, B.1    Casadio, R.2    Fariselli, P.3
  • 13
    • 0030759333 scopus 로고    scopus 로고
    • Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method
    • Cserzo,M., Wallin,E., Simon,I., von Heijne,G. and Elofsson,A. (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method. Protein Eng., 10, 673-676.
    • (1997) Protein Eng. , vol.10 , pp. 673-676
    • Cserzo, M.1    Wallin, E.2    Simon, I.3    von Heijne, G.4    Elofsson, A.5
  • 14
    • 53249092142 scopus 로고    scopus 로고
    • Prediction of membrane protein topology utilizing multiple sequence alignments
    • Persson,B. and Argos,P. (1997) Prediction of membrane protein topology utilizing multiple sequence alignments. J. Protein Chem., 16, 453-457.
    • (1997) J. Protein Chem. , vol.16 , pp. 453-457
    • Persson, B.1    Argos, P.2
  • 15
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin,L.J., Bryson,K. and Jones,D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 16
    • 0031826040 scopus 로고    scopus 로고
    • SOSUI: Classification and secondary structure prediction system for membrane proteins
    • Hirokawa,T., Boon-Chieng,S. and Mitaku,S. (1998) SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378-379.
    • (1998) Bioinformatics , vol.14 , pp. 378-379
    • Hirokawa, T.1    Boon-Chieng, S.2    Mitaku, S.3
  • 17
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
    • Tusnady,G.E. and Simon,I. (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 283, 489-506.
    • (1998) J. Mol. Biol. , vol.283 , pp. 489-506
    • Tusnady, G.E.1    Simon, I.2
  • 18
    • 0031614678 scopus 로고    scopus 로고
    • A hidden Markov model for predicting transmembrane helices in protein sequences
    • Glasgow,J., Littlejohn,T., Major,F., Lathrop,R., Sankoff,D. and Sensen,C. (eds), AAAI Press, Menlo Park, California
    • Sonnhammer,E.L., von Heijne,G. and Krogh,A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In Glasgow,J., Littlejohn,T., Major,F., Lathrop,R., Sankoff,D. and Sensen,C. (eds), Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, California, pp. 175-182.
    • (1998) Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology , pp. 175-182
    • Sonnhammer, E.L.1    von Heijne, G.2    Krogh, A.3
  • 19
    • 0031793227 scopus 로고    scopus 로고
    • Prediction of membrane proteins based on classification of transmembrane segments
    • Kihara,D., Shimizu,T. and Kanehisa,M. (1998) Prediction of membrane proteins based on classification of transmembrane segments. Protein Eng., 11, 961-970.
    • (1998) Protein Eng. , vol.11 , pp. 961-970
    • Kihara, D.1    Shimizu, T.2    Kanehisa, M.3
  • 20
    • 0032989348 scopus 로고    scopus 로고
    • A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: The PRED-TMR algorithm
    • Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J. (1999) A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein Eng., 12, 381-385.
    • (1999) Protein Eng. , vol.12 , pp. 381-385
    • Pasquier, C.1    Promponas, V.J.2    Palaios, G.A.3    Hamodrakas, J.S.4    Hamodrakas, S.J.5
  • 21
    • 0034888209 scopus 로고    scopus 로고
    • A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: The OrienTM algorithm
    • Liakopoulos,T.D., Pasquier,C. and Hamodrakas,S.J. (2001) A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein Eng., 14, 387-390.
    • (2001) Protein Eng. , vol.14 , pp. 387-390
    • Liakopoulos, T.D.1    Pasquier, C.2    Hamodrakas, S.J.3
  • 22
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnady,G.E. and Simon,I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
    • (2001) Bioinformatics , vol.17 , pp. 849-850
    • Tusnady, G.E.1    Simon, I.2
  • 23
    • 0034899781 scopus 로고    scopus 로고
    • Evaluation of methods for the prediction of membrane spanning regions
    • Moeller,S., Croning,M.D. and Apweiler,R. (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 17, 646-653.
    • (2001) Bioinformatics , vol.17 , pp. 646-653
    • Moeller, S.1    Croning, M.D.2    Apweiler, R.3
  • 24
    • 0036132818 scopus 로고    scopus 로고
    • Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using dataset of experimentally-characterized transmembrane topologies
    • Ikeda,M., Arai,M., Lao,D.M. and Shimizu,T. (2002) Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using dataset of experimentally-characterized transmembrane topologies. In Silico, Biol., 2, 19-33.
    • (2002) In Silico, Biol. , vol.2 , pp. 19-33
    • Ikeda, M.1    Arai, M.2    Lao, D.M.3    Shimizu, T.4
  • 25
    • 0001911218 scopus 로고    scopus 로고
    • State-of-the-art in membrane protein prediction
    • Chen,C.P. and Rost,B. (2002) State-of-the-art in membrane protein prediction. Appl. Bioinformatics, 1, 21-35.
    • (2002) Appl. Bioinformatics , vol.1 , pp. 21-35
    • Chen, C.P.1    Rost, B.2
  • 26
    • 0001617290 scopus 로고
    • Construction of a membrane protein database and an evaluation of several prediction methods of transmembrane segments
    • Miyano,S., Akutsu,T., Imai,H., Gotoh,O. and Takagi,T. (eds), Universal Academy Press, Tokyo
    • Shimizu,T. and Nakai,K. (1994) Construction of a membrane protein database and an evaluation of several prediction methods of transmembrane segments. In Miyano,S., Akutsu,T., Imai,H., Gotoh,O. and Takagi,T. (eds), Proceedings of Genome Informatics Workshop 1994. Universal Academy Press, Tokyo, pp. 148-149.
    • (1994) Proceedings of Genome Informatics Workshop 1994 , pp. 148-149
    • Shimizu, T.1    Nakai, K.2
  • 28
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 31
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 32
    • 0034495418 scopus 로고    scopus 로고
    • A collection of well characterised integral membrane proteins
    • Moeller,S., Kriventseva,E.V. and Apweiler,R. (2000) A collection of well characterised integral membrane proteins. Bioinformatics, 16, 1159-1160.
    • (2000) Bioinformatics , vol.16 , pp. 1159-1160
    • Moeller, S.1    Kriventseva, E.V.2    Apweiler, R.3
  • 33
    • 0035109170 scopus 로고    scopus 로고
    • MPtopo: A database of membrane protein topology
    • Jayasinghe,S., Hristova,K. and White,S.H. (2001) MPtopo: A database of membrane protein topology. Protein Sci., 10, 455-458.
    • (2001) Protein Sci. , vol.10 , pp. 455-458
    • Jayasinghe, S.1    Hristova, K.2    White, S.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.