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Volumn 18, Issue 3, 2000, Pages 283-287

Structural genomics and its importance for gene function analysis

Author keywords

Functional motifs; Protein folding; Protein function prediction; Structural genomics; Threading

Indexed keywords

GENE FUNCTION; GENE SEQUENCE; GENE TECHNOLOGY; MOLECULAR EVOLUTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

EID: 0034060287     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/73723     Document Type: Review
Times cited : (190)

References (59)
  • 1
    • 0033083072 scopus 로고    scopus 로고
    • Comparative genomics: The key to understanding the Human Genome Project
    • Clark, M.S. Comparative genomics: the key to understanding the Human Genome Project. Bioessays 21, 121-130 (1999).
    • (1999) Bioessays , vol.21 , pp. 121-130
    • Clark, M.S.1
  • 2
    • 0033575371 scopus 로고    scopus 로고
    • Nutritional genomics: Manipulating plant micronutrients to improve human health
    • DellaPenna, D. Nutritional genomics: manipulating plant micronutrients to improve human health. Science 285, 375-379 (1999).
    • (1999) Science , vol.285 , pp. 375-379
    • DellaPenna, D.1
  • 3
    • 0031720889 scopus 로고    scopus 로고
    • Genomics in the real world
    • Wiley, S.R. Genomics in the real world. Curr. Pharm. Des. 4, 417-422 (1998).
    • (1998) Curr. Pharm. Des. , vol.4 , pp. 417-422
    • Wiley, S.R.1
  • 4
    • 0033520409 scopus 로고    scopus 로고
    • Whole-genome shotgun optical mapping of Deinococcus radiodurans
    • Lin, J. et al. Whole-genome shotgun optical mapping of Deinococcus radiodurans. Science 285, 1558-1562 (1999).
    • (1999) Science , vol.285 , pp. 1558-1562
    • Lin, J.1
  • 5
    • 0032415093 scopus 로고    scopus 로고
    • High throughput analysis of differential gene expression
    • Carulli, J. P. et al. High throughput analysis of differential gene expression. J. Cell Biochem. Suppl. 31, 286-96 (1998).
    • (1998) J. Cell Biochem. Suppl. , vol.31 , pp. 286-296
    • Carulli, J.P.1
  • 6
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • Chothia, C. & Finkelstein, A. The classification and origins of protein folding patterns. Annu. Rev. Biochem. 59, 1007-1039 (1990).
    • (1990) Annu. Rev. Biochem. , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.2
  • 7
    • 0028330220 scopus 로고
    • Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures
    • Murzin, A.G., Lesk, A.M. & Chothia, C. Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures. J. Mol. Biol. 236, 1382-1400 (1994).
    • (1994) J. Mol. Biol. , vol.236 , pp. 1382-1400
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 9
    • 0031787022 scopus 로고    scopus 로고
    • 100,000 protein structures for the biologist
    • Sali, A. 100,000 protein structures for the biologist (see comments). Nat. Struct. Biol. 5, 1029-1032 (1998).
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 1029-1032
    • Sali, A.1
  • 10
    • 0032919371 scopus 로고    scopus 로고
    • Protein folds and families: Sequence and structure alignments
    • Holm, L. & Sander, C. Protein folds and families: sequence and structure alignments. Nucleic Acids Res. 27, 244-247 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 244-247
    • Holm, L.1    Sander, C.2
  • 11
    • 0031841279 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments and family profiles
    • Dodge, C., Schneider, R. & Sander, C. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 26, 313-315 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 313-315
    • Dodge, C.1    Schneider, R.2    Sander, C.3
  • 12
    • 0030765455 scopus 로고    scopus 로고
    • Dali/FSSP classification of three-dimensional folds
    • Holm, L. & Sander, C. Dali/FSSP classification of three-dimensional folds. Nucleic Acids Res. 25, 231-234 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 231-234
    • Holm, L.1    Sander, C.2
  • 13
    • 0030777303 scopus 로고    scopus 로고
    • CATH - A hierarchic classification of protein domain structures
    • Orengo, C.A. et al. CATH - a hierarchic classification of protein domain structures. Structure 5, 1093-1108 (1997).
    • (1997) Structure , vol.5 , pp. 1093-1108
    • Orengo, C.A.1
  • 14
    • 0028961335 scopus 로고
    • Scop: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. Scop: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 (1995).
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 15
    • 0031307019 scopus 로고    scopus 로고
    • Evaluation of comparative protein structure modeling by MODELLER-3
    • Sanchez, R. & Sali, A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins Suppl. 50-58 (1997).
    • (1997) Proteins , Issue.SUPPL. , pp. 50-58
    • Sanchez, R.1    Sali, A.2
  • 16
    • 0029744121 scopus 로고    scopus 로고
    • Molecular similarity based on DOCK-generated fingerprints
    • Briem, H. & Kuntz, I. D. Molecular similarity based on DOCK-generated fingerprints. J. Med. Chem. 39, 3401-3408 (1996).
    • (1996) J. Med. Chem. , vol.39 , pp. 3401-3408
    • Briem, H.1    Kuntz, I.D.2
  • 17
    • 0032483312 scopus 로고    scopus 로고
    • Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/ thioredoxins and T1 ribonucleases
    • Fetrow, J.S. & Skolnick, J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/ thioredoxins and T1 ribonucleases. J. Mol. Biol. 281, 949-968 (1998).
    • (1998) J. Mol. Biol. , vol.281 , pp. 949-968
    • Fetrow, J.S.1    Skolnick, J.2
  • 18
    • 0032475938 scopus 로고    scopus 로고
    • Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity
    • Fetrow, J.S., Godzik, A. & Skolnick, J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 282, 703-711 (1998).
    • (1998) J. Mol. Biol. , vol.282 , pp. 703-711
    • Fetrow, J.S.1    Godzik, A.2    Skolnick, J.3
  • 19
    • 0032843737 scopus 로고    scopus 로고
    • Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily
    • Fetrow, J.S., Siew, N. & Skolnick, J. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. FASEB J. 13, 1866-1874(1999).
    • (1999) FASEB J. , vol.13 , pp. 1866-1874
    • Fetrow, J.S.1    Siew, N.2    Skolnick, J.3
  • 20
    • 0032411227 scopus 로고    scopus 로고
    • Functional analysis of E. coli proteins for members of the a/b hydrolase family
    • Zhang, L., Godzik, A., Skolnick, J. & Fetrow, J.S. Functional analysis of E. coli proteins for members of the a/b hydrolase family. Folding and Design 3, 535-548 (1998).
    • (1998) Folding and Design , vol.3 , pp. 535-548
    • Zhang, L.1    Godzik, A.2    Skolnick, J.3    Fetrow, J.S.4
  • 22
    • 0032921818 scopus 로고    scopus 로고
    • Structural genomics: Keystone for a Human Proteome Project
    • Montelione, G.T. & Andersen, S. Structural genomics: keystone for a Human Proteome Project (news). Nat. Struct. Biol. 6, 11-12 (1999).
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 11-12
    • Montelione, G.T.1    Andersen, S.2
  • 23
    • 0031928367 scopus 로고    scopus 로고
    • Shining a light on structural genomics
    • Kim, S.H. Shining a light on structural genomics. Nat. Struct. Biol. 5 Suppl, 643-645 (1998).
    • (1998) Nat. Struct. Biol. , vol.5 , Issue.SUPPL. , pp. 643-645
    • Kim, S.H.1
  • 24
    • 0344109574 scopus 로고    scopus 로고
    • Structural genomics taking shape
    • Gaasterland, T. Structural genomics taking shape. Trends Genet. 14, 135 (1998).
    • (1998) Trends Genet. , vol.14 , pp. 135
    • Gaasterland, T.1
  • 25
    • 0032506030 scopus 로고    scopus 로고
    • Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
    • Sanchez, R. & Sali, A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Prac. Natl. Acad. Sci. USA 95, 13597-13602 (1998).
    • (1998) Prac. Natl. Acad. Sci. USA , vol.95 , pp. 13597-13602
    • Sanchez, R.1    Sali, A.2
  • 26
  • 27
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of intergral membrane proteins from eubacterial, archaen, and eukaryotic organismc
    • Wallin, E. & Heijne, G.V. Genome-wide analysis of intergral membrane proteins from eubacterial, archaen, and eukaryotic organismc. Prof. Sci. 7, 1029-1038 (1998).
    • (1998) Prof. Sci. , vol.7 , pp. 1029-1038
    • Wallin, E.1    Heijne, G.V.2
  • 28
    • 10244239321 scopus 로고    scopus 로고
    • Life with 6000 genes
    • Goffeau, A. et al. Life with 6000 genes (see comments). Science 274, 546, 563-567 (1996).
    • (1996) Science , vol.274 , pp. 546
    • Goffeau, A.1
  • 29
    • 0032787618 scopus 로고    scopus 로고
    • A comparison of sequence and structure protein domain families as a basis for structural genomics
    • Elofsson, A. & Sonnhammer, E.L. A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics 15, 480-500 (1999).
    • (1999) Bioinformatics , vol.15 , pp. 480-500
    • Elofsson, A.1    Sonnhammer, E.L.2
  • 30
    • 0031577260 scopus 로고    scopus 로고
    • Protein fold recognition by prediction-based threading
    • Rost, B., Schneider, R. & Sander, C. Protein fold recognition by prediction-based threading. J. Mol. Biol. 270, 471-480 (1997).
    • (1997) J. Mol. Biol. , vol.270 , pp. 471-480
    • Rost, B.1    Schneider, R.2    Sander, C.3
  • 31
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones, D.T. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815 (1999).
    • (1999) J. Mol. Biol. , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 32
    • 0032605880 scopus 로고    scopus 로고
    • Comparison of prediction quality in the three CASPs
    • Marchler-Bauer, A. & Brenner, S. Comparison of prediction quality in the three CASPs. Proteins Suppl. 3, 218-225 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 218-225
    • Marchler-Bauer, A.1    Brenner, S.2
  • 33
    • 0030724017 scopus 로고    scopus 로고
    • Assigning folds to the proteins encoded by the genome of Mycoplasme genitalium
    • Fischer, D. & Eisenberg, D, Assigning folds to the proteins encoded by the genome of Mycoplasme genitalium. Proc. Natl. Acad Sci USA 94, 11929-11934 (1997).
    • (1997) Proc. Natl. Acad Sci USA , vol.94 , pp. 11929-11934
    • Fischer, D.1    Eisenberg, D.2
  • 34
    • 0032706408 scopus 로고    scopus 로고
    • A method for the improvement of threading based protein models
    • Kolinski, A., Rotkiewicz, P., Ilkowski, I. & Skolnick, J. A method for the improvement of threading based protein models. Proteins 37, 592-610 (1999).
    • (1999) Proteins , vol.37 , pp. 592-610
    • Kolinski, A.1    Rotkiewicz, P.2    Ilkowski, I.3    Skolnick, J.4
  • 35
    • 0032605909 scopus 로고    scopus 로고
    • Calculation of protein conformation by global optimiation of a potential energy function
    • Lee, J., Liwo, A., Ripoll, D.R., Pillardy, J. & Scheraga, H.A. Calculation of protein conformation by global optimiation of a potential energy function. Proteins Suppl. 3, 204-208 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 204-208
    • Lee, J.1    Liwo, A.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 36
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio structure prediction of CASP III targets using ROSETTA
    • Simons, K.T., Bonneau, R., Ruczinski, I. & Baker, D. Ab initio structure prediction of CASP III targets using ROSETTA. Proteins Suppl. 3, 171-176 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 37
    • 0032613288 scopus 로고    scopus 로고
    • Ab intio folding of proteins using restraints derived from evolutionary information
    • Ortiz, A., Kolinski, A., Rotkiewicz, P., Ilkowski, B. & Skolnick, J. Ab intio folding of proteins using restraints derived from evolutionary information. Proteins Suppl. 3, 177-185 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 177-185
    • Ortiz, A.1    Kolinski, A.2    Rotkiewicz, P.3    Ilkowski, B.4    Skolnick, J.5
  • 38
    • 0032620117 scopus 로고    scopus 로고
    • Improved ab initio predictions with a simplified, flexible geometry model
    • Osguthorpe, D.J. Improved ab initio predictions with a simplified, flexible geometry model. Proteins Suppl. 3, 186-193 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 186-193
    • Osguthorpe, D.J.1
  • 39
    • 0032606133 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using a combined hierarchical approach
    • Samudrala, R., Xia, Y, Huang, E. & Levitt, M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins Suppl 3, 194-198 (1999).
    • (1999) Proteins Suppl , vol.3 , pp. 194-198
    • Samudrala, R.1    Xia, Y.2    Huang, E.3    Levitt, M.4
  • 40
    • 0032828469 scopus 로고    scopus 로고
    • Analysis and assessment of ab initio three-dimensional prediction, secondary structure and contacts prediction
    • Orengo, C., Bray, J.E., LoConte, L. & Sillitoe, I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure and contacts prediction. Proteins Suppl. 3, 149-170 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 149-170
    • Orengo, C.1    Bray, J.E.2    LoConte, L.3    Sillitoe, I.4
  • 41
    • 0032605908 scopus 로고    scopus 로고
    • Structure classification-based assessement of CASP3 prediction for the fold recognition targets
    • Murzin, A. Structure classification-based assessement of CASP3 prediction for the fold recognition targets. Proteins Suppl. 3, 88-103 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 88-103
    • Murzin, A.1
  • 42
    • 0032606076 scopus 로고    scopus 로고
    • Some measures of comparative performance in the three CASPs
    • Venclovas, C., Zemla, A., Fidelis, K. & Moult, J. Some measures of comparative performance in the three CASPs. Proteins Suppl. 3, 231-227 (1999).
    • (1999) Proteins Suppl. , vol.3 , pp. 231-1227
    • Venclovas, C.1    Zemla, A.2    Fidelis, K.3    Moult, J.4
  • 43
    • 0032082048 scopus 로고    scopus 로고
    • Genomics and computational molecular biology
    • Brutlag, D.L. Genomics and computational molecular biology. Curr. Opin. Microbiol. 1, 340-345 (1998).
    • (1998) Curr. Opin. Microbiol. , vol.1 , pp. 340-345
    • Brutlag, D.L.1
  • 44
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 45
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • Pearson, W.R. Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276, 71-84 (1998).
    • (1998) J. Mol. Biol. , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 46
    • 0033119399 scopus 로고    scopus 로고
    • Errors m genome annotation
    • Brenner, S.E. Errors m genome annotation. Trends Genet. 15, 132-133 (1999).
    • (1999) Trends Genet. , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 47
    • 0030752032 scopus 로고    scopus 로고
    • Novel developments with the PRINTS protein fingerprint database
    • Attwood, T.K. et al. Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res. 25, 212-216 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 212-216
    • Attwood, T.K.1
  • 48
    • 0025882349 scopus 로고
    • Prosite: A dictionary of sites and patterns in proteins
    • Bairoch, A. Prosite: a dictionary of sites and patterns in proteins. Nucleic Acids Res. Suppl, 19, 2241-2245 (1991).
    • (1991) Nucleic Acids Res. , vol.19 , Issue.SUPPL. , pp. 2241-2245
    • Bairoch, A.1
  • 51
    • 0029916916 scopus 로고    scopus 로고
    • The Blocks database - A system for protein classification
    • Pietrovski, S., Henikoff, J.G. & Henikoff, S. The Blocks database - a system for protein classification. Nucleic Acids Res. 24, 197-200 (1996).
    • (1996) Nucleic Acids Res. , vol.24 , pp. 197-200
    • Pietrovski, S.1    Henikoff, J.G.2    Henikoff, S.3
  • 52
    • 0031678064 scopus 로고    scopus 로고
    • A homology identification method that combines protein sequence and structure information
    • Yu, L., White, J.V. & Smith, T.F. A homology identification method that combines protein sequence and structure information. Protein Sci. 7, 2499-2510 (1998).
    • (1998) Protein Sci. , vol.7 , pp. 2499-2510
    • Yu, L.1    White, J.V.2    Smith, T.F.3
  • 53
    • 0033548460 scopus 로고    scopus 로고
    • Three-dimensional structure analyis of Prosite patterns
    • Kasuya, A. & Thornton, J.M. Three-dimensional structure analyis of Prosite patterns. J. Mol. Biol. 286, 1673-1691 (1999).
    • (1999) J. Mol. Biol. , vol.286 , pp. 1673-1691
    • Kasuya, A.1    Thornton, J.M.2
  • 54
    • 0033597176 scopus 로고    scopus 로고
    • The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
    • Hegyi, H. & Gerstein, M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288, 147-164 (1999).
    • (1999) J. Mol. Biol. , vol.288 , pp. 147-164
    • Hegyi, H.1    Gerstein, M.2
  • 55
    • 0029973830 scopus 로고    scopus 로고
    • Derivation of 3d coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
    • Wallace, A.C., Laskowski, R.A. & Thornton, J.M. Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5, 1001-1013 (1996).
    • (1996) Protein Sci. , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 56
    • 0028230909 scopus 로고
    • Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: Potential implications to evolution and to protein folding
    • Fischer, D., Wolfson, H., Lin, S.L. & Nussinov, R. Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Sci. 3, 769-778 (1994).
    • (1994) Protein Sci. , vol.3 , pp. 769-778
    • Fischer, D.1    Wolfson, H.2    Lin, S.L.3    Nussinov, R.4
  • 57
    • 0028235532 scopus 로고
    • Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein
    • Matthews, D.A. et al. Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77, 761-771 (1994).
    • (1994) Cell , vol.77 , pp. 761-771
    • Matthews, D.A.1
  • 58
    • 0032431024 scopus 로고    scopus 로고
    • Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics
    • Zarembinski, T.I. et al. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc. Natl. Acad. Sci. USA 95, 15189-15193 (1998).
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 15189-15193
    • Zarembinski, T.I.1
  • 59
    • 0032922524 scopus 로고    scopus 로고
    • The PRESAGE database for structural genomics
    • Brenner, S.E., Barken, D. & Levitt, M. The PRESAGE database for structural genomics. Nucleic Acids Res. 27, 251-253 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 251-253
    • Brenner, S.E.1    Barken, D.2    Levitt, M.3


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