메뉴 건너뛰기




Volumn 60, Issue 12, 2003, Pages 2637-2650

Automatic prediction of protein function

Author keywords

Ab initio prediction; Bioinformatics; Genome analysis; Multiple alignments; Neural networks; Post translational modifications; Protein function prediction; Protein protein interactions; Sequence analysis; Subcellular localization

Indexed keywords

AB INITIO CALCULATION; BIOINFORMATICS; CHEMICAL REACTION; GENOME ANALYSIS; PREDICTION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; REVIEW; SEQUENCE ANALYSIS; TASK PERFORMANCE;

EID: 0346731042     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00018-003-3114-8     Document Type: Review
Times cited : (208)

References (180)
  • 2
    • 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
  • 3
    • 0037250635 scopus 로고    scopus 로고
    • PEP: Predictions for entire proteomes
    • Carter P., Liu J. and Rost B. (2003) PEP: predictions for entire proteomes. Nucleic Acids Res. 31: 410-413
    • (2003) Nucleic Acids Res. , vol.31 , pp. 410-413
    • Carter, P.1    Liu, J.2    Rost, B.3
  • 5
    • 0347890404 scopus 로고    scopus 로고
    • Reference removed in proof
    • Reference removed in proof
  • 6
    • 0035814904 scopus 로고    scopus 로고
    • Computational genomics
    • Koonin E. V. (2001) Computational genomics. Curr. Biol. 11: R155-R158
    • (2001) Curr. Biol. , vol.11
    • Koonin, E.V.1
  • 7
    • 0034734040 scopus 로고    scopus 로고
    • Automated extraction of information in molecular biology
    • Andrade M. A. and Bork P. (2000) Automated extraction of information in molecular biology. FEBS Lett. 476: 12-17
    • (2000) FEBS Lett. , vol.476 , pp. 12-17
    • Andrade, M.A.1    Bork, P.2
  • 9
    • 0344417851 scopus 로고    scopus 로고
    • A novel method for automatic functional annotation of proteins
    • Fleischmann W., Moller S., Gateau A. and Apweiler R. (1999) A novel method for automatic functional annotation of proteins. Bioinformatics 15: 228-233
    • (1999) Bioinformatics , vol.15 , pp. 228-233
    • Fleischmann, W.1    Moller, S.2    Gateau, A.3    Apweiler, R.4
  • 10
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNa interactions at an atomic level
    • Luscombe N. M., Laskowski R. A. and Thornton J. M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29: 2860-2874
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 11
    • 0035874906 scopus 로고    scopus 로고
    • From genome to function
    • Thornton J. M. (2001) From genome to function. Science 292: 2095-2097
    • (2001) Science , vol.292 , pp. 2095-2097
    • Thornton, J.M.1
  • 12
    • 0032919371 scopus 로고    scopus 로고
    • Protein folds and families: Sequence and structure alignments
    • Holm L. and Sander C. (1999) Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27: 244-247
    • (1999) Nucleic Acids Res. , vol.27 , pp. 244-247
    • Holm, L.1    Sander, C.2
  • 13
    • 0036947904 scopus 로고    scopus 로고
    • Bioinformatics: Biology by other means
    • Valencia A. (2002) Bioinformatics: biology by other means. Bioinformatics 18: 1551-1552
    • (2002) Bioinformatics , vol.18 , pp. 1551-1552
    • Valencia, A.1
  • 14
    • 0036601150 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein interactions
    • Valencia A. and Pazos F. (2002) Computational methods for the prediction of protein interactions. Curr. Opin. Str. Biol. 12: 368-373
    • (2002) Curr. Opin. Str. Biol. , vol.12 , pp. 368-373
    • Valencia, A.1    Pazos, F.2
  • 15
    • 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
  • 19
    • 0033008596 scopus 로고    scopus 로고
    • Distribution of protein folds in the three superkingdoms of life
    • Wolf Y., Brenner S., Bash P. and Koonin E. (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res. 9: 17-26
    • (1999) Genome Res. , vol.9 , pp. 17-26
    • Wolf, Y.1    Brenner, S.2    Bash, P.3    Koonin, E.4
  • 20
    • 0030720480 scopus 로고    scopus 로고
    • A structural census of the current population of protein sequences
    • Gerstein M. and Levitt M. (1997) A structural census of the current population of protein sequences. Proc. Natl. Acad. Sci. USA 94: 11911-11916
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11911-11916
    • Gerstein, M.1    Levitt, M.2
  • 25
    • 0346799108 scopus 로고    scopus 로고
    • Prediction of protein function from protein sequence and structure
    • in press
    • Whisstock J. C. and Lesk A. M. (2003) Prediction of protein function from protein sequence and structure. Quart. Rev. Biophys. in press
    • (2003) Quart. Rev. Biophys.
    • Whisstock, J.C.1    Lesk, A.M.2
  • 26
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari G., Sander C. and Valencia A. (1995) A method to predict functional residues in proteins. Nat. Struct. Biol. 2: 171-178
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 27
    • 0037470597 scopus 로고    scopus 로고
    • Automatic methods for predicting functionally important residues
    • del Sol Mesa A., Pazos F. and Valencia A. (2003) Automatic methods for predicting functionally important residues. J. Mol. Biol. 326: 1289-1302
    • (2003) J. Mol. Biol. , vol.326 , pp. 1289-1302
    • Del Sol Mesa, A.1    Pazos, F.2    Valencia, A.3
  • 28
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O., Bourne H. R. and Cohen F. E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257: 342-358
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 29
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge O. and Sowa M. E. (2002) Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Str. Biol. 12: 21-27
    • (2002) Curr. Opin. Str. Biol. , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 30
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko T., Bell R. E., Mayrose I., Glaser F. and Ben-Tal N. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18: S71-S77
    • (2002) Bioinformatics , vol.18
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 31
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser F., Pupko T., Paz I., Bell R. E., Bechor-Shental D., Martz E. et al. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6
  • 33
    • 0036174712 scopus 로고    scopus 로고
    • Continuum secondary structure captures protein flexibility
    • Andersen C. A. F., Palmer A. G., Brunak S. and Rost B. (2002) Continuum secondary structure captures protein flexibility. Structure 10: 175-184
    • (2002) Structure , vol.10 , pp. 175-184
    • Andersen, C.A.F.1    Palmer, A.G.2    Brunak, S.3    Rost, B.4
  • 37
    • 0033926482 scopus 로고    scopus 로고
    • Protein sequence databases
    • Apweiler R. (2000) Protein sequence databases. Adv. Protein Chem. 54: 31-71
    • (2000) Adv. Protein Chem. , vol.54 , pp. 31-71
    • Apweiler, R.1
  • 38
    • 0037174288 scopus 로고    scopus 로고
    • Bioinformatics methods for the analysis of expression arrays: Data clustering and information extraction
    • Tamames J., Clark D., Herrero J., Dopazo J., Blaschke C., Fernandez J. M. et al. (2002) Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J. Biotechnol. 98: 269-283
    • (2002) J. Biotechnol. , vol.98 , pp. 269-283
    • Tamames, J.1    Clark, D.2    Herrero, J.3    Dopazo, J.4    Blaschke, C.5    Fernandez, J.M.6
  • 39
  • 40
    • 0036122694 scopus 로고    scopus 로고
    • Online genomics facilities in the new millennium
    • Frishman D., Kaps A. and Mewes H. W. (2002) Online genomics facilities in the new millennium. Pharmacogenomics 3: 265-271
    • (2002) Pharmacogenomics , vol.3 , pp. 265-271
    • Frishman, D.1    Kaps, A.2    Mewes, H.W.3
  • 42
    • 0037305939 scopus 로고    scopus 로고
    • Domains, motifs and clusters in the protein universe
    • Liu J. and Rost B. (2003) Domains, motifs and clusters in the protein universe. Curr. Opin. Chem. Biol. 7: 5-11
    • (2003) Curr. Opin. Chem. Biol. , vol.7 , pp. 5-11
    • Liu, J.1    Rost, B.2
  • 44
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol. 318: 595-608
    • (2002) J. Mol. Biol. , vol.318 , pp. 595-608
    • Rost, B.1
  • 45
    • 0032950094 scopus 로고    scopus 로고
    • KIND-a non-redundant protein database
    • Kallberg Y. and Persson B. (1999) KIND-a non-redundant protein database. Bioinformatics 15: 260-261
    • (1999) Bioinformatics , vol.15 , pp. 260-261
    • Kallberg, Y.1    Persson, B.2
  • 46
    • 0037250525 scopus 로고    scopus 로고
    • Improvements to CluSTr: The database of SWISS-PROT+TrEMBL protein clusters
    • Kriventseva E. V., Servant F. and Apweiler R. (2003) Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. Nucleic Acids Res. 31: 388-389
    • (2003) Nucleic Acids Res. , vol.31 , pp. 388-389
    • Kriventseva, E.V.1    Servant, F.2    Apweiler, R.3
  • 47
    • 0032776495 scopus 로고    scopus 로고
    • Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
    • Henikoff S., Henikoff J. G. and Pietrokovski S. (1999) Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 15: 471-479
    • (1999) Bioinformatics , vol.15 , pp. 471-479
    • Henikoff, S.1    Henikoff, J.G.2    Pietrokovski, S.3
  • 49
    • 0035072551 scopus 로고    scopus 로고
    • Clustering of highly homologous sequences to reduce the size of large protein databases
    • Li W., Jaroszewski L. and Godzik A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17: 282-283
    • (2001) Bioinformatics , vol.17 , pp. 282-283
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 50
    • 0043122933 scopus 로고    scopus 로고
    • UniqueProt: Creating representative protein sequence sets
    • Mika S. and Rost B. (2003) UniqueProt: creating representative protein sequence sets. Nucleic Acids Res. 31: 3789-3791
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3789-3791
    • Mika, S.1    Rost, B.2
  • 52
    • 0029828166 scopus 로고    scopus 로고
    • Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
    • Gaasterland T. and Sensen C. W. (1996) Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie 78: 302-310
    • (1996) Biochimie , vol.78 , pp. 302-310
    • Gaasterland, T.1    Sensen, C.W.2
  • 54
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The gene ontology consortium
    • Ashburner M., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P. et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25: 25-29
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1    Blake, J.A.2    Botstein, D.3    Butler, H.4    Cherry, J.M.5    Davis, A.P.6
  • 55
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd A. E., Orengo C. A. and Thornton J. M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307: 1113-1143
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 57
    • 0345998940 scopus 로고    scopus 로고
    • Cataloguing proteins in cell cycle control
    • Lieberman, H. (ed), Humana Press, Totowa, NJ
    • Wrzeszczynski K. O. and Rost B. (2003) Cataloguing proteins in cell cycle control. In: Cell Cycle Checkpoint Control Protocols, pp. 219-233, Lieberman, H. (ed), Humana Press, Totowa, NJ
    • (2003) Cell Cycle Checkpoint Control Protocols , pp. 219-233
    • Wrzeszczynski, K.O.1    Rost, B.2
  • 58
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • Devos D. and Valencia A. (2000) Practical limits of function prediction. Proteins 41: 98-107
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 59
    • 0036891705 scopus 로고    scopus 로고
    • Sequence conserved for sub-cellular localization
    • Nair R. and Rost B. (2002) Sequence conserved for sub-cellular localization. Protein Sci. 11: 2836-2847
    • (2002) Protein Sci. , vol.11 , pp. 2836-2847
    • Nair, R.1    Rost, B.2
  • 62
    • 0034677669 scopus 로고    scopus 로고
    • Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
    • Wilson C. A., Kreychman J. and Gerstein M. (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297: 233-249
    • (2000) J. Mol. Biol. , vol.297 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 63
    • 0347890403 scopus 로고    scopus 로고
    • Reference removed in proof
    • Reference removed in proof
  • 67
    • 0033042327 scopus 로고    scopus 로고
    • Whole-genome sequence annotation: 'Going wrong with confidence'
    • Kyrpides N. C. and Ouzounis C. A. (1999) Whole-genome sequence annotation: 'Going wrong with confidence'. Mol. Microbiol. 32: 886-887
    • (1999) Mol. Microbiol. , vol.32 , pp. 886-887
    • Kyrpides, N.C.1    Ouzounis, C.A.2
  • 68
    • 18144453832 scopus 로고    scopus 로고
    • Errors in genome reviews
    • Kyrpides N. C. and Ouzounis C. A. (1998) Errors in genome reviews. Science 281: 1457
    • (1998) Science , vol.281 , pp. 1457
    • Kyrpides, N.C.1    Ouzounis, C.A.2
  • 69
    • 0034133732 scopus 로고    scopus 로고
    • Annotations of biochemically uncharacterized open reading frames (ORFs)
    • Mushegian A. R. (2000) Annotations of biochemically uncharacterized open reading frames (ORFs). Mol. Microbiol. 35: 697-698
    • (2000) Mol. Microbiol. , vol.35 , pp. 697-698
    • Mushegian, A.R.1
  • 71
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos D. and Valencia A. (2001) Intrinsic errors in genome annotation. Trends Genet. 17: 429-431
    • (2001) Trends Genet. , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 72
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin M. Y. and Koonin E. V. (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol. 1: 55-67
    • (1998) In Silico Biol. , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 73
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner S. E. (1999) Errors in genome annotation. Trends Genet. 15: 132-133
    • (1999) Trends Genet. , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 74
    • 0035753660 scopus 로고    scopus 로고
    • Quod erat demonstrandum? the mystery of experimental validation of apparently erroneous computational analyses of protein sequences
    • RESEARCH0051
    • Iyer L. M., Aravind L., Bork P., Hofmann K., Mushegian A. R., Zhulin I. B. et al. (2001) Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol. 2: RESEARCH0051
    • (2001) Genome Biol. , vol.2
    • Iyer, L.M.1    Aravind, L.2    Bork, P.3    Hofmann, K.4    Mushegian, A.R.5    Zhulin, I.B.6
  • 75
    • 0003410183 scopus 로고
    • Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, Academic Press, New York
    • Webb E. C. (1992) Enzyme Nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, Academic Press, New York
    • (1992) Enzyme Nomenclature 1992
    • Webb, E.C.1
  • 77
    • 0031887946 scopus 로고    scopus 로고
    • Wanted: Subcellular localization of proteins based on sequence
    • Eisenhaber F. and Bork P. (1998) Wanted: subcellular localization of proteins based on sequence. Trends Cell Biol. 8: 169-170
    • (1998) Trends Cell Biol. , vol.8 , pp. 169-170
    • Eisenhaber, F.1    Bork, P.2
  • 78
    • 0034828777 scopus 로고    scopus 로고
    • Functional versatility and molecular diversity of the metabolic map of Escherichia coli
    • Tsoka S. and Ouzounis C. A. (2001) Functional versatility and molecular diversity of the metabolic map of Escherichia coli. Genome Res. 11: 1503-1510
    • (2001) Genome Res. , vol.11 , pp. 1503-1510
    • Tsoka, S.1    Ouzounis, C.A.2
  • 79
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. (1999) Twilight zone of protein sequence alignments. Prot. Eng. 12: 85-94
    • (1999) Prot. Eng. , vol.12 , pp. 85-94
    • Rost, B.1
  • 80
    • 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
  • 81
    • 0029868212 scopus 로고    scopus 로고
    • Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site
    • Nielsen H., Engelbrecht J., von Heijne G. and Brunak S. (1996) Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site. Proteins 24: 165-177
    • (1996) Proteins , vol.24 , pp. 165-177
    • Nielsen, H.1    Engelbrecht, J.2    Von Heijne, G.3    Brunak, S.4
  • 82
    • 0030801002 scopus 로고    scopus 로고
    • Gapped Blast and PSI-Blast: A new generation of protein database search programs
    • Altschul S., Madden T., Shaffer A., Zhang J., Zhang Z., Miller W. et al. (1997) Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.1    Madden, T.2    Shaffer, A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6
  • 84
    • 0036467068 scopus 로고    scopus 로고
    • Alignments grow, secondary structure prediction improves
    • Przybylski D. and Rost B. (2002) Alignments grow, secondary structure prediction improves. Proteins 46: 195-205
    • (2002) Proteins , vol.46 , pp. 195-205
    • Przybylski, D.1    Rost, B.2
  • 86
    • 0037249633 scopus 로고    scopus 로고
    • The TIGR-FAMs database of protein families
    • Haft D. H., Selengut J. D. and White O. (2003) The TIGR-FAMs database of protein families. Nucleic Acids Res. 31: 371-373
    • (2003) Nucleic Acids Res. , vol.31 , pp. 371-373
    • Haft, D.H.1    Selengut, J.D.2    White, O.3
  • 87
    • 0031707505 scopus 로고    scopus 로고
    • Nucleocytoplasmic transport: The soluble phase
    • Mattaj I. W. and Englmeier L. (1998) Nucleocytoplasmic transport: the soluble phase. Annu. Rev. Biochem. 67: 265-306
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 265-306
    • Mattaj, I.W.1    Englmeier, L.2
  • 88
    • 0029979607 scopus 로고    scopus 로고
    • Common principles of protein translocation across membranes
    • Schatz G. and Dobberstein B. (1996) Common principles of protein translocation across membranes. Science 271: 1519-1526
    • (1996) Science , vol.271 , pp. 1519-1526
    • Schatz, G.1    Dobberstein, B.2
  • 89
    • 0034664730 scopus 로고    scopus 로고
    • The debate about transport in the Golgi - Two sides of the same coin?
    • Pelham H. R. and Rothman J. E. (2000) The debate about transport in the Golgi - two sides of the same coin? Cell 102: 713-719
    • (2000) Cell , vol.102 , pp. 713-719
    • Pelham, H.R.1    Rothman, J.E.2
  • 90
    • 0033909566 scopus 로고    scopus 로고
    • Protein sorting signals and prediction of subcellular localization
    • Nakai K. (2000) Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem. 54: 277-344
    • (2000) Adv. Protein Chem. , vol.54 , pp. 277-344
    • Nakai, K.1
  • 91
    • 0033044637 scopus 로고    scopus 로고
    • Machine learning approaches for the prediction of signal peptides and other protein sorting signals
    • Nielsen H., Brunak S. and von Heijne G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Prot. Eng. 12: 3-9
    • (1999) Prot. Eng. , vol.12 , pp. 3-9
    • Nielsen, H.1    Brunak, S.2    Von Heijne, G.3
  • 92
    • 0035229330 scopus 로고    scopus 로고
    • Analysis and prediction of mitochondrial targeting peptides
    • Emanuelsson O., von Heijne G. and Schneider G. (2001) Analysis and prediction of mitochondrial targeting peptides. Methods Cell Biol. 65: 175-187
    • (2001) Methods Cell Biol. , vol.65 , pp. 175-187
    • Emanuelsson, O.1    Von Heijne, G.2    Schneider, G.3
  • 93
    • 0033738137 scopus 로고    scopus 로고
    • A comparison of signal sequence prediction methods using a test set of signal peptides
    • Menne K. M., Hermjakob H. and Apweiler R. (2000) A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics 16: 741-742
    • (2000) Bioinformatics , vol.16 , pp. 741-742
    • Menne, K.M.1    Hermjakob, H.2    Apweiler, R.3
  • 94
    • 0032077533 scopus 로고    scopus 로고
    • Using neural networks for prediction of the subcellular location of proteins
    • Reinhardt A. and Hubbard T. (1998) Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res. 26: 2230-2235
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2230-2235
    • Reinhardt, A.1    Hubbard, T.2
  • 95
    • 0035367127 scopus 로고    scopus 로고
    • Whole-genome analysis: Annotations and updates
    • Gaasterland T. and Oprea M. (2001) Whole-genome analysis: annotations and updates. Curr. Opin. Str. Biol. 11: 377-381
    • (2001) Curr. Opin. Str. Biol. , vol.11 , pp. 377-381
    • Gaasterland, T.1    Oprea, M.2
  • 96
    • 0034331073 scopus 로고    scopus 로고
    • Finding nuclear localisation signals
    • Cokol M., Nair R. and Rost B. (2000) Finding nuclear localisation signals. EMBO Rep. 1: 411-415
    • (2000) EMBO Rep. , vol.1 , pp. 411-415
    • Cokol, M.1    Nair, R.2    Rost, B.3
  • 97
    • 0037249644 scopus 로고    scopus 로고
    • NLSdb: Database of nuclear localization signals
    • Nair R., Carter P. and Rost B. (2003) NLSdb: database of nuclear localization signals. Nucleic Acids Res. 31: 397-399
    • (2003) Nucleic Acids Res. , vol.31 , pp. 397-399
    • Nair, R.1    Carter, P.2    Rost, B.3
  • 98
    • 0020132173 scopus 로고
    • Correlation of the amino acid composition of a protein to its structural and biological characteristics
    • Nishikawa K. and Ooi T. (1982) Correlation of the amino acid composition of a protein to its structural and biological characteristics. J. Biochem. 91: 1821-1824
    • (1982) J. Biochem. , vol.91 , pp. 1821-1824
    • Nishikawa, K.1    Ooi, T.2
  • 99
    • 0026521552 scopus 로고
    • The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins
    • Nakashima H. and Nishikawa K. (1992) The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Lett. 303: 141-146
    • (1992) FEBS Lett. , vol.303 , pp. 141-146
    • Nakashima, H.1    Nishikawa, K.2
  • 100
    • 0025933503 scopus 로고
    • Expert system for predicting protein localization sites in gram-negative bacteria
    • Nakai K. and Kanehisa M. (1991) Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11: 95-110
    • (1991) Proteins , vol.11 , pp. 95-110
    • Nakai, K.1    Kanehisa, M.2
  • 101
    • 0027105007 scopus 로고
    • A knowledge base for predicting protein localization sites in eukaryotic cells
    • Nakai K. and Kanehisa M. (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911
    • (1992) Genomics , vol.14 , pp. 897-911
    • Nakai, K.1    Kanehisa, M.2
  • 103
    • 0029915525 scopus 로고
    • Computational method to predict mitochondrially imported proteins and their transit peptides
    • Claros M. G. and Vincens P. (1995) Computational method to predict mitochondrially imported proteins and their transit peptides. Eur. J. Biochem. 241: 779-786
    • (1995) Eur. J. Biochem. , vol.241 , pp. 779-786
    • Claros, M.G.1    Vincens, P.2
  • 104
    • 0034843744 scopus 로고    scopus 로고
    • Support vector machine approach for protein subcellular localization prediction
    • Hua S. and Sun Z. (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17: 721-728
    • (2001) Bioinformatics , vol.17 , pp. 721-728
    • Hua, S.1    Sun, Z.2
  • 105
    • 0031588694 scopus 로고    scopus 로고
    • Relation between amino acid composition and cellular location of proteins
    • Cedano J., Aloy P., Pérez-Pons J. A. and Querol E. (1997) Relation between amino acid composition and cellular location of proteins. J. Mol. Biol. 266: 594-600
    • (1997) J. Mol. Biol. , vol.266 , pp. 594-600
    • Cedano, J.1    Aloy, P.2    Pérez-Pons, J.A.3    Querol, E.4
  • 106
    • 0036677029 scopus 로고    scopus 로고
    • Predicting protein cellular localization using a domain projection method
    • Mott R., Schultz J., Bork P. and Ponting C. P. (2002) Predicting protein cellular localization using a domain projection method. Genome Res. 12: 1168-1174
    • (2002) Genome Res. , vol.12 , pp. 1168-1174
    • Mott, R.1    Schultz, J.2    Bork, P.3    Ponting, C.P.4
  • 108
    • 0032972509 scopus 로고    scopus 로고
    • PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization
    • Nakai K. and Horton P. (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24: 34-36
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 34-36
    • Nakai, K.1    Horton, P.2
  • 109
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H., Engelbrecht J., Brunak S. and von Heijne G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Prot. Eng. 10: 1-6
    • (1997) Prot. Eng. , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Von Heijne, G.4
  • 110
    • 0032935861 scopus 로고    scopus 로고
    • ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
    • Emanuelsson O., Nielsen H. and von Heijne G. (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8: 978-984
    • (1999) Protein Sci. , vol.8 , pp. 978-984
    • Emanuelsson, O.1    Nielsen, H.2    Von Heijne, G.3
  • 111
    • 0034714135 scopus 로고    scopus 로고
    • A Bayesian system integrating expression data with sequence patterns for localizing proteins: Comprehensive application to the yeast genome
    • Drawid A. and Gerstein M. (2000) A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol. 301: 1059-1075
    • (2000) J. Mol. Biol. , vol.301 , pp. 1059-1075
    • Drawid, A.1    Gerstein, M.2
  • 112
    • 0344118117 scopus 로고    scopus 로고
    • Better prediction of sub-cellular localization by combining evolutionary and structural information
    • in press
    • Nair R. and Rost B. (2003) Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins, in press
    • (2003) Proteins
    • Nair, R.1    Rost, B.2
  • 113
    • 0037250368 scopus 로고    scopus 로고
    • The RESID Database of Protein Modifications: 2003 Developments
    • Garavelli J. S. (2003) The RESID Database of Protein Modifications: 2003 developments. Nucleic Acids Res. 31: 499-501
    • (2003) Nucleic Acids Res. , vol.31 , pp. 499-501
    • Garavelli, J.S.1
  • 114
    • 0025945726 scopus 로고
    • Improving signal peptide prediction accuracy by simulated neural network
    • Ladunga I., Czakó F., Csabai I. and Geszti T. (1991) Improving signal peptide prediction accuracy by simulated neural network. CABIOS 7: 485-487
    • (1991) CABIOS , vol.7 , pp. 485-487
    • Ladunga, I.1    Czakó, F.2    Csabai, I.3    Geszti, T.4
  • 115
    • 0032817742 scopus 로고    scopus 로고
    • How many potentially secreted proteins are contained in a bacterial genome?
    • Schneider G. (1999) How many potentially secreted proteins are contained in a bacterial genome? Gene 237: 113-121
    • (1999) Gene , vol.237 , pp. 113-121
    • Schneider, G.1
  • 116
    • 0034119780 scopus 로고    scopus 로고
    • Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites
    • Jagla B. and Schuchhardt J. (2000) Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites. Bioinformatics 16: 245-250
    • (2000) Bioinformatics , vol.16 , pp. 245-250
    • Jagla, B.1    Schuchhardt, J.2
  • 117
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson O., Nielsen H., Brunak S. and von Heijne G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300: 1005-1016
    • (2000) J. Mol. Biol. , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    Von Heijne, G.4
  • 118
    • 0035782686 scopus 로고    scopus 로고
    • Prediction of in vivo fates of proteins in the era of genomics and proteomics
    • Nakai K. (2001) Prediction of in vivo fates of proteins in the era of genomics and proteomics. J. Struct. Biol. 134: 103-116
    • (2001) J. Struct. Biol. , vol.134 , pp. 103-116
    • Nakai, K.1
  • 119
    • 0032539958 scopus 로고    scopus 로고
    • Peptide design aided by neural networks: Biological activity of artificial signal peptidase I cleavage sites
    • Wrede P., Landt O., Klages S., Fatemi A., Hahn U. and Schneider G. (1998) Peptide design aided by neural networks: biological activity of artificial signal peptidase I cleavage sites. Biochemistry 37: 3588-3593
    • (1998) Biochemistry , vol.37 , pp. 3588-3593
    • Wrede, P.1    Landt, O.2    Klages, S.3    Fatemi, A.4    Hahn, U.5    Schneider, G.6
  • 121
    • 0037089139 scopus 로고    scopus 로고
    • Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites
    • Graber J. H., McAllister G. D. and Smith T. F. (2002) Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites. Nucleic Acids Res. 30: 1851-1858
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1851-1858
    • Graber, J.H.1    McAllister, G.D.2    Smith, T.F.3
  • 122
    • 0031762518 scopus 로고    scopus 로고
    • Artificial neural network method for predicting HIV protease cleavage sites in protein
    • Cai Y. D., Yu H. and Chou K. C. (1998) Artificial neural network method for predicting HIV protease cleavage sites in protein. J. Protein Chem. 17: 607-615
    • (1998) J. Protein Chem. , vol.17 , pp. 607-615
    • Cai, Y.D.1    Yu, H.2    Chou, K.C.3
  • 124
  • 125
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom N., Gammeltoft S. and Brunak S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294: 1351-1362
    • (1999) J. Mol. Biol. , vol.294 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 126
    • 0032922002 scopus 로고    scopus 로고
    • PhosphoBase, a database of phosphorylation sites: Release 2.0
    • Kreegipuu A., Blom N. and Brunak S. (1999) PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res. 27: 237-239
    • (1999) Nucleic Acids Res. , vol.27 , pp. 237-239
    • Kreegipuu, A.1    Blom, N.2    Brunak, S.3
  • 127
    • 0035049164 scopus 로고    scopus 로고
    • Post-translational GPI lipid anchor modification of proteins in kingdoms of life: Analysis of protein sequence data from complete genomes
    • Eisenhaber B., Bork P. and Eisenhaber F. (2001) Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Prot. Eng. 14: 17-25
    • (2001) Prot. Eng. , vol.14 , pp. 17-25
    • Eisenhaber, B.1    Bork, P.2    Eisenhaber, F.3
  • 128
    • 0036370537 scopus 로고    scopus 로고
    • Prediction of glycosylation across the human proteome and the correlation to protein function
    • Gupta R. and Brunak S. (2002) Prediction of glycosylation across the human proteome and the correlation to protein function. Pac. Symp. Biocomput. 310-322
    • (2002) Pac. Symp. Biocomput. , pp. 310-322
    • Gupta, R.1    Brunak, S.2
  • 129
    • 0031809552 scopus 로고    scopus 로고
    • NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
    • Hansen J., Lund O., Tolstrup N., Gooley A. A., Williams K. L. and Brunak S. (1998) NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconjugate J. 15: 115-130
    • (1998) Glycoconjugate J. , vol.15 , pp. 115-130
    • Hansen, J.1    Lund, O.2    Tolstrup, N.3    Gooley, A.A.4    Williams, K.L.5    Brunak, S.6
  • 131
    • 0036290648 scopus 로고    scopus 로고
    • N-terminal N-myristoylation of proteins: Prediction of substrate proteins from amino acid sequence
    • Maurer-Stroh S., Eisenhaber B. and Eisenhaber F. (2002) N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J. Mol. Biol. 317: 541-557
    • (2002) J. Mol. Biol. , vol.317 , pp. 541-557
    • Maurer-Stroh, S.1    Eisenhaber, B.2    Eisenhaber, F.3
  • 132
    • 0027133165 scopus 로고
    • Function of the gene products in Escherichia coli
    • Riley M. (1993) Function of the gene products in Escherichia coli. Microbiol. Rev. 57: 862-952
    • (1993) Microbiol. Rev. , vol.57 , pp. 862-952
    • Riley, M.1
  • 133
    • 0036169141 scopus 로고    scopus 로고
    • Machine learning of functional class from phenotype data
    • Clare A. and King R. D. (2002) Machine learning of functional class from phenotype data. Bioinformatics 18: 160-166
    • (2002) Bioinformatics , vol.18 , pp. 160-166
    • Clare, A.1    King, R.D.2
  • 134
    • 0034084865 scopus 로고    scopus 로고
    • Who's your neighbor? New computational approaches for functional genomics
    • Galperin M. Y. and Koonin E. V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18: 609-613
    • (2000) Nat. Biotechnol. , vol.18 , pp. 609-613
    • Galperin, M.Y.1    Koonin, E.V.2
  • 135
    • 0031024670 scopus 로고    scopus 로고
    • Conserved clusters of functionally related genes in two bacterial genomes
    • Tamames J., Casari G., Ouzounis C. and Valencia A. (1997) Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44
    • (1997) J. Mol. Evol. , vol.44
    • Tamames, J.1    Casari, G.2    Ouzounis, C.3    Valencia, A.4
  • 137
    • 18444390875 scopus 로고    scopus 로고
    • Prediction of human protein function from post-translational modifications and localization features
    • Jensen L. J., Gupta R., Blom N., Devos D., Tamames J., Kesmir C. et al. (2002) Prediction of human protein function from post-translational modifications and localization features. J. Mol. Biol. 319: 1257-1265
    • (2002) J. Mol. Biol. , vol.319 , pp. 1257-1265
    • Jensen, L.J.1    Gupta, R.2    Blom, N.3    Devos, D.4    Tamames, J.5    Kesmir, C.6
  • 138
    • 0036671947 scopus 로고    scopus 로고
    • Copper and prion diseases
    • Brown D. R. (2002) Copper and prion diseases. Biochem. Soc. Trans. 30: 742-745
    • (2002) Biochem. Soc. Trans. , vol.30 , pp. 742-745
    • Brown, D.R.1
  • 139
    • 0036892449 scopus 로고    scopus 로고
    • Prediction of novel archaeal enzymes from sequence-derived features
    • Jensen L. J., Skovgaard M. and Brunak S. (2002) Prediction of novel archaeal enzymes from sequence-derived features. Protein Sci. 11: 2894-2898
    • (2002) Protein Sci. , vol.11 , pp. 2894-2898
    • Jensen, L.J.1    Skovgaard, M.2    Brunak, S.3
  • 140
    • 0037460964 scopus 로고    scopus 로고
    • Prediction of human protein function according to Gene Ontology categories
    • Jensen L. J., Gupta R., Staerfeldt H. H. and Brunak S. (2003) Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19: 635-642
    • (2003) Bioinformatics , vol.19 , pp. 635-642
    • Jensen, L.J.1    Gupta, R.2    Staerfeldt, H.H.3    Brunak, S.4
  • 141
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P., Giot L., Cagney G., Mansfield T. A., Judson R. S., Knight J. R. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.A.4    Judson, R.S.5    Knight, J.R.6
  • 143
    • 0035367880 scopus 로고    scopus 로고
    • Determination of protein function, evolution and interactions by structural genomics
    • Teichmann S. A., Murzin A. G. and Chothia C. (2001) Determination of protein function, evolution and interactions by structural genomics. Curr. Opin. Str. Biol. 11: 354-363
    • (2001) Curr. Opin. Str. Biol. , vol.11 , pp. 354-363
    • Teichmann, S.A.1    Murzin, A.G.2    Chothia, C.3
  • 144
    • 0036306236 scopus 로고    scopus 로고
    • On the role of electrostatic interactions in the design of protein-protein interfaces
    • Sheinerman F. B. and Honig B. (2002) On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mol. Biol. 318: 161-177
    • (2002) J. Mol. Biol. , vol.318 , pp. 161-177
    • Sheinerman, F.B.1    Honig, B.2
  • 145
    • 0034027595 scopus 로고    scopus 로고
    • Computational genetics: Finding protein function by nonhomology methods
    • Marcotte E. M. (2000) Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Str. Biol. 10: 359-365
    • (2000) Curr. Opin. Str. Biol. , vol.10 , pp. 359-365
    • Marcotte, E.M.1
  • 146
    • 0034923505 scopus 로고    scopus 로고
    • Analysis of proteins and proteomes by mass spectrometry
    • Mann M., Hendrickson R. C. and Pandey A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70: 437-473
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 437-473
    • Mann, M.1    Hendrickson, R.C.2    Pandey, A.3
  • 147
    • 0036469060 scopus 로고    scopus 로고
    • Unravelling hot spots in binding interfaces: Progress and challenges
    • DeLano W. (2002) Unravelling hot spots in binding interfaces: progress and challenges. Curr. Opin. Str. Biol. 12: 14-20
    • (2002) Curr. Opin. Str. Biol. , vol.12 , pp. 14-20
    • DeLano, W.1
  • 148
    • 0035424708 scopus 로고    scopus 로고
    • Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments
    • Michnick S. W. (2001) Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments. Curr. Opin. Str. Biol. 11: 472-477
    • (2001) Curr. Opin. Str. Biol. , vol.11 , pp. 472-477
    • Michnick, S.W.1
  • 150
    • 0037250151 scopus 로고    scopus 로고
    • InterDom: A database of putative interacting protein domains for validating predicted protein interactions and complexes
    • Ng S. K., Zhang Z., Tan S. H. and Lin K. (2003) InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res. 31: 251-254
    • (2003) Nucleic Acids Res. , vol.31 , pp. 251-254
    • Ng, S.K.1    Zhang, Z.2    Tan, S.H.3    Lin, K.4
  • 151
    • 0037249217 scopus 로고    scopus 로고
    • Whole-proteome interaction mining
    • Bock J. R. and Gough D. A. (2003) Whole-proteome interaction mining. Bioinformatics 19: 125-134
    • (2003) Bioinformatics , vol.19 , pp. 125-134
    • Bock, J.R.1    Gough, D.A.2
  • 152
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The biomolecular interaction network database
    • Bader G. D., Betel D. and Hogue C. W. (2003) BIND: the biomolecular interaction network database. Nucleic Acids Res. 31: 248-250
    • (2003) Nucleic Acids Res. , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 153
    • 0037250158 scopus 로고    scopus 로고
    • InterPreTS: Protein interaction prediction through tertiary structure
    • Aloy P. and Russell R. B. (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19: 161-162
    • (2003) Bioinformatics , vol.19 , pp. 161-162
    • Aloy, P.1    Russell, R.B.2
  • 154
    • 0037059461 scopus 로고    scopus 로고
    • A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
    • Tong A. H., Drees B., Nardelli G., Bader G. D., Brannetti B., Castagnoli L. et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321-324
    • (2002) Science , vol.295 , pp. 321-324
    • Tong, A.H.1    Drees, B.2    Nardelli, G.3    Bader, G.D.4    Brannetti, B.5    Castagnoli, L.6
  • 155
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith G. R. and Sternberg M. J. (2002) Prediction of protein-protein interactions by docking methods. Curr. Opin. Str. Biol. 12: 28-35
    • (2002) Curr. Opin. Str. Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 156
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin A. C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5    Bauer, A.6
  • 157
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho Y., Gruhler A., Heilbut A., Bader G. D., Moore L., Adams S. L. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.D.4    Moore, L.5    Adams, S.L.6
  • 159
    • 0035755823 scopus 로고    scopus 로고
    • The potential use of SUISEKI as a protein interaction discovery tool
    • Blaschke C. and Valencia A. (2001) The potential use of SUISEKI as a protein interaction discovery tool. Genome Inform. Ser. Workshop Genome Inform. 12: 123-134
    • (2001) Genome Inform. Ser. Workshop Genome Inform. , vol.12 , pp. 123-134
    • Blaschke, C.1    Valencia, A.2
  • 160
    • 0035002541 scopus 로고    scopus 로고
    • Mining literature for protein-protein interactions
    • Marcotte E. M., Xenarios I. and Eisenberg D. (2001) Mining literature for protein-protein interactions. Bioinformatics 17: 359-363
    • (2001) Bioinformatics , vol.17 , pp. 359-363
    • Marcotte, E.M.1    Xenarios, I.2    Eisenberg, D.3
  • 161
    • 0035967862 scopus 로고    scopus 로고
    • Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction
    • Gromiha M. M. and Selvaraj S. (2001) Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J. Mol. Biol. 310: 27-32
    • (2001) J. Mol. Biol. , vol.310 , pp. 27-32
    • Gromiha, M.M.1    Selvaraj, S.2
  • 162
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the database of interacting proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios I., Salwinski L., Duan X. J., Higney P., Kim S. M. and Eisenberg D. (2002) DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30: 303-305
    • (2002) Nucleic Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.M.5    Eisenberg, D.6
  • 164
    • 0034766349 scopus 로고    scopus 로고
    • Mining functional information associated with expression arrays
    • Blaschke C., Oliveros J. C. and Valencia A. (2001) Mining functional information associated with expression arrays. Funct. Integr. Genomics 1: 256-268
    • (2001) Funct. Integr. Genomics , vol.1 , pp. 256-268
    • Blaschke, C.1    Oliveros, J.C.2    Valencia, A.3
  • 165
    • 0035236048 scopus 로고    scopus 로고
    • GENIES : A natural-language processing system for the extraction of molecular pathways from journal articles
    • Friedman C., Kra P., Yu H., Krauthammer M. and Rzhetsky A. (2001) GENIES : a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17: S74-S82
    • (2001) Bioinformatics , vol.17
    • Friedman, C.1    Kra, P.2    Yu, H.3    Krauthammer, M.4    Rzhetsky, A.5
  • 166
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context
    • Huynen M., Snel B., Lathe W. and Bork P. (2000) Predicting protein function by genomic context. Genome Res. 4: 1204-1210
    • (2000) Genome Res. , vol.4 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe, W.3    Bork, P.4
  • 167
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar T., Snel B., Huynen M. and Bork P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324-328
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 168
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte E. M., Pellegrini M., Ng H. L., Rice D. W., Yeates T. O. and Eisenberg D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 169
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright A. J., Ilipoulos I., Kyrpides N. C. and Ouzounis C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Ilipoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 170
    • 0031610846 scopus 로고    scopus 로고
    • Constructing multigenome views of whole microbial genomes
    • Gaasterland T. and Ragan M. A. (1998) Constructing multigenome views of whole microbial genomes. Microb. Comp. Genomics 3: 177-192
    • (1998) Microb. Comp. Genomics , vol.3 , pp. 177-192
    • Gaasterland, T.1    Ragan, M.A.2
  • 171
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • Pazos F. and Valencia A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Prot. Eng. 14: 609-614
    • (2001) Prot. Eng. , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 173
    • 0036435908 scopus 로고    scopus 로고
    • Co-evolutionary analysis reveals insights into protein-protein interactions
    • Goh C. S. and Cohen F. E. (2002) Co-evolutionary analysis reveals insights into protein-protein interactions. J. Mol. Biol. 324: 177-192
    • (2002) J. Mol. Biol. , vol.324 , pp. 177-192
    • Goh, C.S.1    Cohen, F.E.2
  • 174
    • 0030821675 scopus 로고    scopus 로고
    • Correlated mutations contain information about protein-protein interaction
    • Pazos F., Helmer-Citterich M., Ausiello G. and Valencia A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271: 511-523
    • (1997) J. Mol. Biol. , vol.271 , pp. 511-523
    • Pazos, F.1    Helmer-Citterich, M.2    Ausiello, G.3    Valencia, A.4
  • 175
    • 0036568319 scopus 로고    scopus 로고
    • In silico two-hybrid system for the selection of physically interacting protein pairs
    • Pazos F. and Valencia A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47: 219-227
    • (2002) Proteins , vol.47 , pp. 219-227
    • Pazos, F.1    Valencia, A.2
  • 176
    • 0035943340 scopus 로고    scopus 로고
    • Correlated sequence-signatures as markers of protein-protein interaction
    • Sprinzak E. and Margalit H. (2001) Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol. 311: 681-692
    • (2001) J. Mol. Biol. , vol.311 , pp. 681-692
    • Sprinzak, E.1    Margalit, H.2
  • 177
    • 0035672003 scopus 로고    scopus 로고
    • Probabilistic prediction of unknown metabolic and signal-transduction networks
    • Gomez S. M., Lo S. H. and Rzhetsky A. (2001) Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics 159: 1291-1298
    • (2001) Genetics , vol.159 , pp. 1291-1298
    • Gomez, S.M.1    Lo, S.H.2    Rzhetsky, A.3
  • 178
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy P. and Russell R. B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA 99: 5896-5901
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 179
    • 0037110589 scopus 로고    scopus 로고
    • MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
    • Lu L., Lu H. and Skolnick J. (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364
    • (2002) Proteins , vol.49 , pp. 350-364
    • Lu, L.1    Lu, H.2    Skolnick, J.3
  • 180
    • 0344480548 scopus 로고    scopus 로고
    • Inferring sub-cellular localisation through automated lexical analysis
    • Nair, R. and Rost B. (2002) Inferring sub-cellular localisation through automated lexical analysis. Bioinformatics 18: S78-S86
    • (2002) Bioinformatics , vol.18
    • Nair, R.1    Rost, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.