메뉴 건너뛰기




Volumn 32, Issue 12, 2004, Pages 3522-3530

Sequence-based prediction of protein domains

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOCHEMISTRY; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; BIOLOGY; EVALUATION; GENOMICS; METHODOLOGY; PROTEIN TERTIARY STRUCTURE; REPRODUCIBILITY; SEQUENCE ANALYSIS;

EID: 3042810008     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh684     Document Type: Article
Times cited : (80)

References (77)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • The genome international sequencing consortium. Initial sequencing and analysis of the human genome
    • The genome international sequencing consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 3
    • 0032509302 scopus 로고    scopus 로고
    • The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: A platform for investigating biology
    • The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282, 2012-2018.
    • (1998) Science , vol.282 , pp. 2012-2018
  • 5
    • 0029894792 scopus 로고    scopus 로고
    • The yeast genome project: What did we learn?
    • Dujon,B. (1996) The yeast genome project: what did we learn? TIGS, 12, 263-270.
    • (1996) TIGS , vol.12 , pp. 263-270
    • Dujon, B.1
  • 7
    • 0036601151 scopus 로고    scopus 로고
    • Did evolution leap to create the protein universe?
    • Rost,B. (2002) Did evolution leap to create the protein universe? Curr. Opin. Struct. Biol., 12, 409-416.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 409-416
    • Rost, B.1
  • 8
    • 0028114231 scopus 로고
    • Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria
    • Abrahams,J.P., Leslie,A.G., Lutter,R. and Walker,J.E. (1994) Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria. Nature, 370, 621-628.
    • (1994) Nature , vol.370 , pp. 621-628
    • Abrahams, J.P.1    Leslie, A.G.2    Lutter, R.3    Walker, J.E.4
  • 9
    • 0034988805 scopus 로고    scopus 로고
    • Structure of proteins involved in synaptic vesicle fusion in neurons
    • Brunger,A.T. (2001) Structure of proteins involved in synaptic vesicle fusion in neurons. Annu. Rev. Biophys. Biomol. Struct., 30, 157-171.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 157-171
    • Brunger, A.T.1
  • 10
    • 0023506457 scopus 로고
    • Folding and association of proteins
    • Jaennicke,R. (1987) Folding and association of proteins. Prog. Biophys. Mol. Biol., 49, 117-237.
    • (1987) Prog. Biophys. Mol. Biol. , vol.49 , pp. 117-237
    • Jaennicke, R.1
  • 11
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm,L. and Sander,C. (1994) Parser for protein folding units. Proteins, 19, 256-268.
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 13
  • 14
    • 0141757323 scopus 로고    scopus 로고
    • Reprogramming control of an allosteric signaling switch through modular recombination
    • Dueber,J.E., Yeh,B.J., Chak,K. and Lim,W.A. (2003) Reprogramming control of an allosteric signaling switch through modular recombination. Science, 301, 1904-1908.
    • (2003) Science , vol.301 , pp. 1904-1908
    • Dueber, J.E.1    Yeh, B.J.2    Chak, K.3    Lim, W.A.4
  • 17
    • 0032189646 scopus 로고    scopus 로고
    • Dictionary of recurrent domains in protein structures
    • Holm,L. and Sander,C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88-96.
    • (1998) Proteins , vol.33 , pp. 88-96
    • Holm, L.1    Sander, C.2
  • 19
    • 0034682851 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments
    • Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol., 301, 691-711.
    • (2000) J. Mol. Biol. , vol.301 , pp. 691-711
    • Yang, A.S.1    Honig, B.2
  • 20
    • 0031889752 scopus 로고    scopus 로고
    • Domain assignment for protein structures using a consensus approach: Characterizatibn and analysis
    • Jones,S., Stewart,M., Michie,A.D., Swindells,M.B., Orengo,C.A. and Thornton,J.M. (1998) Domain assignment for protein structures using a consensus approach: characterizatibn and analysis. Protein Sci., 7, 233-242.
    • (1998) Protein Sci. , vol.7 , pp. 233-242
    • Jones, S.1    Stewart, M.2    Michie, A.D.3    Swindells, M.B.4    Orengo, C.A.5    Thornton, J.M.6
  • 21
    • 0021769523 scopus 로고
    • The prediction of protein domains
    • Busetta,B. and Barrans,Y. (1984) The prediction of protein domains. Biochim. Biophys. Acta, 790, 117-124.
    • (1984) Biochim. Biophys. Acta , vol.790 , pp. 117-124
    • Busetta, B.1    Barrans, Y.2
  • 22
    • 0023058984 scopus 로고
    • A possible way for prediction of domain boundaries in globular proteins from amino acid sequence
    • Vonderviszt,F. and Simon,I. (1986) A possible way for prediction of domain boundaries in globular proteins from amino acid sequence. Biochem. Biophys. Res. Commun., 139, 11-17.
    • (1986) Biochem. Biophys. Res. Commun. , vol.139 , pp. 11-17
    • Vonderviszt, F.1    Simon, I.2
  • 23
    • 0024057934 scopus 로고
    • Prediction of the location of structural domains in globular proteins
    • Kikuchi,T., Nemethy,G. and Scheraga,H.A. (1988) Prediction of the location of structural domains in globular proteins. J. Protein Chem., 7, 427-471.
    • (1988) J. Protein Chem. , vol.7 , pp. 427-471
    • Kikuchi, T.1    Nemethy, G.2    Scheraga, H.A.3
  • 24
    • 0033957841 scopus 로고    scopus 로고
    • ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
    • Corpet,F., Servant,F., Gouzy,J. and Kahn,D. (2000) ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res., 28, 267-269.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 267-269
    • Corpet, F.1    Servant, F.2    Gouzy, J.3    Kahn, D.4
  • 26
    • 0031812904 scopus 로고    scopus 로고
    • The ProDom database of protein domain families
    • Corpet,F., Gouzy,F. and Kahn,D. (1998) The ProDom database of protein domain families. Nucleic Acids Res., 26, 323-326.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 323-326
    • Corpet, F.1    Gouzy, F.2    Kahn, D.3
  • 27
    • 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
  • 28
    • 0032436341 scopus 로고    scopus 로고
    • DOMO: A new database of aligned protein domains
    • Gracy,J. and Argos,P. (1998) DOMO: a new database of aligned protein domains. TIBS, 23, 495-497.
    • (1998) TIBS , vol.23 , pp. 495-497
    • Gracy, J.1    Argos, P.2
  • 29
    • 0036721254 scopus 로고    scopus 로고
    • Protein domain identification and improved sequence similarity searching using PSI-BLAST
    • George,R.A. and Heringa,J. (2002) Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins, 48, 672-681.
    • (2002) Proteins , vol.48 , pp. 672-681
    • George, R.A.1    Heringa, J.2
  • 33
  • 35
    • 0036083833 scopus 로고    scopus 로고
    • The SBASE protein domain library, release 9.0: An online resource for protein domain identification
    • Vlahovicek,K., Murvai,J., Barta,E. and Pongor,S. (2002) The SBASE protein domain library, release 9.0: an online resource for protein domain identification. Nucleic Acids Res., 30, 273-275.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 273-275
    • Vlahovicek, K.1    Murvai, J.2    Barta, E.3    Pongor, S.4
  • 37
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough,J., Karplus,K., Hughey,R. and Chothia,C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
    • (2001) J. Mol. Biol. , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 38
    • 12244311255 scopus 로고    scopus 로고
    • PFDB: A generic protein family database integrating the CATH domain structure database with sequence based protein family resources
    • Shepherd,A.J., Martin,N.J., Johnson,R.G., Kellam,P. and Orengo,C.A. (2002) PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics, 18, 1666-1672.
    • (2002) Bioinformatics , vol.18 , pp. 1666-1672
    • Shepherd, A.J.1    Martin, N.J.2    Johnson, R.G.3    Kellam, P.4    Orengo, C.A.5
  • 40
    • 84888070567 scopus 로고    scopus 로고
    • Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods
    • Kulikowski,C.A., Muchnik,I., Yun,H.J., Dayanik,A.A., Zhang,D., Song,Y. and Montelione,G.T. (2001) Protein structural domain parsing by consensus reasoning over multiple knowledge sources and methods. Medinfo, 10, 965-969.
    • (2001) Medinfo , vol.10 , pp. 965-969
    • Kulikowski, C.A.1    Muchnik, I.2    Yun, H.J.3    Dayanik, A.A.4    Zhang, D.5    Song, Y.6    Montelione, G.T.7
  • 41
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignant algorithms with structure alignments
    • Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr (2000) Large-scale comparison of protein sequence alignant algorithms with structure alignments. Proteins, 40, 6-22.
    • (2000) Proteins , vol.40 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack Jr., R.L.3
  • 42
    • 2442499624 scopus 로고    scopus 로고
    • CHOP proteins into structural domain-like fragments
    • Liu,J. and Rost,B. (2004) CHOP proteins into structural domain-like fragments. Proteins, 55, 678-688.
    • (2004) Proteins , vol.55 , pp. 678-688
    • Liu, J.1    Rost, B.2
  • 43
    • 0033753811 scopus 로고    scopus 로고
    • Domain size distributions can predict domain boundaries
    • Wheelan,S.J., Marchler-Bauer,A. and Bryant,S.H. (2000) Domain size distributions can predict domain boundaries. Bioinformatics, 16, 613-618.
    • (2000) Bioinformatics , vol.16 , pp. 613-618
    • Wheelan, S.J.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 44
    • 0036306348 scopus 로고    scopus 로고
    • SnapDRAGON: A method to delineate protein structural domains from sequence data
    • George,R.A. and Heringa,J. (2002) SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol., 316, 839-851.
    • (2002) J. Mol. Biol. , vol.316 , pp. 839-851
    • George, R.A.1    Heringa, J.2
  • 45
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • Aszodi,A., Gradwell,M.J. and Taylor,W.R. (1995) Global fold determination from a small number of distance restraints. J. Mol. Biol., 251, 308-326.
    • (1995) J. Mol. Biol. , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 46
    • 0032951163 scopus 로고    scopus 로고
    • Protein structural domain identification
    • Taylor,W.R. (1999) Protein structural domain identification. Protein Eng., 12, 203-216.
    • (1999) Protein Eng. , vol.12 , pp. 203-216
    • Taylor, W.R.1
  • 47
    • 0036893072 scopus 로고    scopus 로고
    • Rapid protein domain assignment from amino acid sequence using predicted secondary structure
    • Marsden,R.L., McGuffin,L.J. and Jones,D.T. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci., 11, 2814-2824.
    • (2002) Protein Sci. , vol.11 , pp. 2814-2824
    • Marsden, R.L.1    McGuffin, L.J.2    Jones, D.T.3
  • 50
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
    • (1999) Protein Eng. , vol.12 , pp. 85-94
    • Rost, B.1
  • 51
    • 0026030641 scopus 로고
    • Database of homology-derived structures and the structural meaning of sequence alignment
    • Sander,C. and Schneider,R. (1991) Database of homology-derived structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 52
    • 0034682894 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence
    • Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol., 301, 679-689.
    • (2000) J. Mol. Biol. , vol.301 , pp. 679-689
    • Yang, A.S.1    Honig, B.2
  • 55
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost,B. and Sander,C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 56
    • 0028300741 scopus 로고
    • Combining evolutionary information and neural networks to predict protein secondary structure
    • Rost,B. and Sander,C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19, 55-72.
    • (1994) Proteins , vol.19 , pp. 55-72
    • Rost, B.1    Sander, C.2
  • 57
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost,B. and Sander,C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226.
    • (1994) Proteins , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 58
    • 0029889988 scopus 로고    scopus 로고
    • PHD: Predicting one-dimensional protein structure by profile based neural networks
    • Rost,B. (1996) PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol., 266, 525-539.
    • (1996) Methods Enzymol. , vol.266 , pp. 525-539
    • Rost, B.1
  • 59
    • 0030038634 scopus 로고    scopus 로고
    • Topology prediction for helical transmembrane proteins at 86% accuracy
    • Rost,B., Casadio,R. and Fariselli,P. (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci., 5, 1704-1718.
    • (1996) Protein Sci. , vol.5 , pp. 1704-1718
    • Rost, B.1    Casadio, R.2    Fariselli, P.3
  • 60
    • 0038356582 scopus 로고    scopus 로고
    • Predict protein-protein interaction sites from local sequence information
    • Ofran,Y. and Rost,B. (2003) Predict protein-protein interaction sites from local sequence information. FEBS Lett., 544, 236-239.
    • (2003) FEBS Lett. , vol.544 , pp. 236-239
    • Ofran, Y.1    Rost, B.2
  • 61
    • 0028158628 scopus 로고
    • PHD-an automatic server for protein secondary structure prediction
    • Rost,B., Sander,C. and Schneider,R. (1994) PHD-an automatic server for protein secondary structure prediction. CABIOS, 10, 53-60.
    • (1994) CABIOS , vol.10 , pp. 53-60
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 62
    • 0028361031 scopus 로고
    • Accuracy of protein flexibility predictions
    • Vihinen,M., Torkkila,E. and Riikonen,P. (1994) Accuracy of protein flexibility predictions. Proteins, 19, 141-149.
    • (1994) Proteins , vol.19 , pp. 141-149
    • Vihinen, M.1    Torkkila, E.2    Riikonen, P.3
  • 63
    • 3242891265 scopus 로고    scopus 로고
    • CHOP: Parsing proteins into structural domains
    • Liu,J. and Rost,B. (2004)CHOP: parsing proteins into structural domains. Nucleic Acids Res., 32, W569-W571.
    • (2004) Nucleic Acids Res. , vol.32
    • Liu, J.1    Rost, B.2
  • 64
    • 0036288851 scopus 로고    scopus 로고
    • Characterization and prediction of linker sequences of multi-domain proteins by a neural network
    • Miyazaki,S., Kuroda,Y. and Yokoyama,S. (2002) Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J. Struct. Funct. Gen., 2, 37-51.
    • (2002) J. Struct. Funct. Gen. , vol.2 , pp. 37-51
    • Miyazaki, S.1    Kuroda, Y.2    Yokoyama, S.3
  • 67
    • 0033762915 scopus 로고    scopus 로고
    • Structural genomics programs at the US National Institute of General Medical Sciences
    • Norvell,J.C. and Machalek,A.Z. (2000) Structural genomics programs at the US National Institute of General Medical Sciences. Nature Struct. Biol., (Suppl 7), 931.
    • (2000) Nature Struct. Biol. , Issue.SUPPL. 7 , pp. 931
    • Norvell, J.C.1    Machalek, A.Z.2
  • 68
    • 0344109574 scopus 로고    scopus 로고
    • Structural genomics taking shape
    • Gaasterland,T. (1998) Structural genomics taking shape. TIGS, 14, 135.
    • (1998) TIGS , vol.14 , pp. 135
    • Gaasterland, T.1
  • 69
    • 0031787022 scopus 로고    scopus 로고
    • 100 000 protein structures for the biologist
    • Sali,A. (1998) 100 000 protein structures for the biologist. Nature Struct. Biol., 5, 1029-1032.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 1029-1032
    • Sali, A.1
  • 70
    • 0032521218 scopus 로고    scopus 로고
    • Marrying structure and genomics
    • Rost,B. (1998) Marrying structure and genomics. Structure, 6, 259-263.
    • (1998) Structure , vol.6 , pp. 259-263
    • Rost, B.1
  • 71
    • 0032922524 scopus 로고    scopus 로고
    • The PRESAGE database for structural genomics
    • Brenner,S.E., Barken,D. and Levitt,M. (1999) The PRESAGE database for structural genomics. Nucleic Acids Res., 27, 251-253.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 251-253
    • Brenner, S.E.1    Barken, D.2    Levitt, M.3
  • 74
    • 0033730342 scopus 로고    scopus 로고
    • Methodologies for target selection in structural genomics
    • Linial,M. and Yona,G. (2000) Methodologies for target selection in structural genomics. Prog. Biophys. Mol. Biol., 73, 297-320.
    • (2000) Prog. Biophys. Mol. Biol. , vol.73 , pp. 297-320
    • Linial, M.1    Yona, G.2
  • 75
    • 0036322695 scopus 로고    scopus 로고
    • Target space for structural genomics revisited
    • Liu,J. and Rost,B. (2002) Target space for structural genomics revisited. Bioinformatics, 18, 922-933.
    • (2002) Bioinformatics , vol.18 , pp. 922-933
    • Liu, J.1    Rost, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.