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Volumn 14, Issue 3, 2004, Pages 307-312

The interplay of fold recognition and experimental structure determination in structural genomics

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS SUBTILIS; CAENORHABDITIS; CAENORHABDITIS ELEGANS; DATA BASE; GENE SEQUENCE; GENE STRUCTURE; GENOMICS; HIGH THROUGHPUT SCREENING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; THERMOTOGA MARITIMA;

EID: 2942576133     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.04.005     Document Type: Review
Times cited : (31)

References (44)
  • 2
    • 0032521199 scopus 로고    scopus 로고
    • The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science
    • Shapiro L., Lima C.D. The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science. Structure. 6:1998;265-267
    • (1998) Structure , vol.6 , pp. 265-267
    • Shapiro, L.1    Lima, C.D.2
  • 3
    • 0031787022 scopus 로고    scopus 로고
    • 100,000 protein structures for the biologist
    • Sali A. 100, 000 protein structures for the biologist. Nat Struct Biol. 5:1998;1029-1032
    • (1998) Nat Struct Biol , vol.5 , pp. 1029-1032
    • Sali, A.1
  • 5
    • 0035487690 scopus 로고    scopus 로고
    • A tour of structural genomics
    • Brenner S.E. A tour of structural genomics. Nat Rev Genet. 2:2001;801-809
    • (2001) Nat Rev Genet , vol.2 , pp. 801-809
    • Brenner, S.E.1
  • 7
    • 2942605788 scopus 로고    scopus 로고
    • The Protein Structure Initiative on World Wide Web URL: http://www.nigms.nih.gov/psi/
  • 10
    • 0033730342 scopus 로고    scopus 로고
    • Methodologies for target selection in structural genomics
    • Linial M., Yona G. Methodologies for target selection in structural genomics. Prog Biophys Mol Biol. 73:2000;297-320
    • (2000) Prog Biophys Mol Biol , vol.73 , pp. 297-320
    • Linial, M.1    Yona, G.2
  • 11
    • 0034674175 scopus 로고    scopus 로고
    • Estimating the number of protein folds and families from complete genome data
    • Wolf Y.I., Grishin N.V., Koonin E.V. Estimating the number of protein folds and families from complete genome data. J Mol Biol. 299:2000;897-905
    • (2000) J Mol Biol , vol.299 , pp. 897-905
    • Wolf, Y.I.1    Grishin, N.V.2    Koonin, E.V.3
  • 12
    • 0036322695 scopus 로고    scopus 로고
    • Target space for structural genomics revisited
    • Liu J., Rost B. Target space for structural genomics revisited. Bioinformatics. 18:2002;922-933
    • (2002) Bioinformatics , vol.18 , pp. 922-933
    • Liu, J.1    Rost, B.2
  • 13
    • 0242292029 scopus 로고    scopus 로고
    • More for less in structural genomics
    • Heger A., Holm L. More for less in structural genomics. J Struct Funct Genomics. 4:2003;57-66
    • (2003) J Struct Funct Genomics , vol.4 , pp. 57-66
    • Heger, A.1    Holm, L.2
  • 14
    • 0041418213 scopus 로고    scopus 로고
    • Flavors of protein disorder
    • A review of pioneering efforts in the prediction of protein disorder.
    • Vucetic S., Brown C.J., Dunker A.K., Obradovic Z. Flavors of protein disorder. Proteins. 52:2003;573-584 A review of pioneering efforts in the prediction of protein disorder.
    • (2003) Proteins , vol.52 , pp. 573-584
    • Vucetic, S.1    Brown, C.J.2    Dunker, A.K.3    Obradovic, Z.4
  • 15
    • 0242458482 scopus 로고    scopus 로고
    • Protein disorder prediction: Implications for structural proteomics
    • A survey of the most pressing, unexpected problem for both structural genomics and structure prediction efforts - the existence of proteins with no well-defined unique structure.
    • Linding R., Jensen L.J., Diella F., Bork P., Gibson T.J., Russell R.B. Protein disorder prediction: implications for structural proteomics. Structure. 11:2003;1453-1459 A survey of the most pressing, unexpected problem for both structural genomics and structure prediction efforts - the existence of proteins with no well-defined unique structure.
    • (2003) Structure , vol.11 , pp. 1453-1459
    • Linding, R.1    Jensen, L.J.2    Diella, F.3    Bork, P.4    Gibson, T.J.5    Russell, R.B.6
  • 16
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:2001;93-96
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 17
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski L., Jaroszewski L., Li W., Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9:2000;232-241
    • (2000) Protein Sci , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 18
    • 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., Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 313:2001;903-919
    • (2001) J Mol Biol , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 20
    • 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. 287:1999;797-815
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 23
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • Sonnhammer E.L., Eddy S.R., Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 28:1997;405-420
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 25
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • A short review of the current champion of fold recognition approaches - jury systems that develop consensus predictions based on individual methods.
    • Ginalski K., Elofsson A., Fischer D., Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics. 19:2003;1015-1018 A short review of the current champion of fold recognition approaches - jury systems that develop consensus predictions based on individual methods.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 26
    • 0242369082 scopus 로고    scopus 로고
    • Raptor: Optimal protein threading by linear programming
    • A new breath of life in genuine, structure-based threading. Novel algorithms based on an integer programming approach make a dent in the problem of optimizing an alignment with a non-local scoring function.
    • Xu J., Li M., Kim D., Xu Y. Raptor: optimal protein threading by linear programming. J Bioinformatics Computat Biol. 1:2003;95-119 A new breath of life in genuine, structure-based threading. Novel algorithms based on an integer programming approach make a dent in the problem of optimizing an alignment with a non-local scoring function.
    • (2003) J Bioinformatics Computat Biol , vol.1 , pp. 95-119
    • Xu, J.1    Li, M.2    Kim, D.3    Xu, Y.4
  • 27
    • 0037414465 scopus 로고    scopus 로고
    • Exhaustive enumeration of protein domain families
    • ADDA, an automated domain decomposition and clustering algorithm, provides a detailed list of possible structural genomics targets, albeit at a relatively low threshold for clustering (which results in a very high number of potential targets).
    • Heger A., Holm L. Exhaustive enumeration of protein domain families. J Mol Biol. 328:2003;749-767 ADDA, an automated domain decomposition and clustering algorithm, provides a detailed list of possible structural genomics targets, albeit at a relatively low threshold for clustering (which results in a very high number of potential targets).
    • (2003) J Mol Biol , vol.328 , pp. 749-767
    • Heger, A.1    Holm, L.2
  • 29
    • 0043163718 scopus 로고    scopus 로고
    • Protein families and TRIBES in genome sequence space
    • Enright A.J., Kunin V., Ouzounis C.A. Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31:2003;4632-4638
    • (2003) Nucleic Acids Res , vol.31 , pp. 4632-4638
    • Enright, A.J.1    Kunin, V.2    Ouzounis, C.A.3
  • 30
    • 0141634362 scopus 로고    scopus 로고
    • Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    • Sadreyev R.I., Baker D., Grishin N.V. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci. 12:2003;2262-2272
    • (2003) Protein Sci , vol.12 , pp. 2262-2272
    • Sadreyev, R.I.1    Baker, D.2    Grishin, N.V.3
  • 31
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona G., Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol. 315:2002;1257-1275
    • (2002) J Mol Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 32
    • 1842559320 scopus 로고    scopus 로고
    • Alignment of protein sequences by their profiles
    • Marti-Renom M.A., Madhusudhan M.S., Sali A. Alignment of protein sequences by their profiles. Protein Sci. 13:2004;1071-1087
    • (2004) Protein Sci , vol.13 , pp. 1071-1087
    • Marti-Renom, M.A.1    Madhusudhan, M.S.2    Sali, A.3
  • 33
    • 2942544229 scopus 로고    scopus 로고
    • COACH: Profile-profile alignment of protein families using hidden Markov models
    • in press.
    • Edgar RC, Sjolander K: COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics 2004, in press.
    • (2004) Bioinformatics
    • Edgar, R.C.1    Sjolander, K.2
  • 34
    • 0037248878 scopus 로고    scopus 로고
    • The Protein Data Bank and structural genomics
    • A description of the paradigm-redefining resource developed by the structural genomics community - a database of structure determination targets, complete with information on failures and secrets about future plans.
    • Westbrook J., Feng Z., Chen L., Yang H., Berman H.M. The Protein Data Bank and structural genomics. Nucleic Acids Res. 31:2003;489-491 A description of the paradigm-redefining resource developed by the structural genomics community - a database of structure determination targets, complete with information on failures and secrets about future plans.
    • (2003) Nucleic Acids Res , vol.31 , pp. 489-491
    • Westbrook, J.1    Feng, Z.2    Chen, L.3    Yang, H.4    Berman, H.M.5
  • 35
    • 9144261138 scopus 로고    scopus 로고
    • Mining the structural genomics pipeline: Identification of protein properties that affect high-throughput experimental analysis
    • Goh C.S., Lan N., Douglas S.M., Wu B., Echols N., Smith A., Milburn D., Montelione G.T., Zhao H., Gerstein M. Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol. 336:2004;115-130
    • (2004) J Mol Biol , vol.336 , pp. 115-130
    • Goh, C.S.1    Lan, N.2    Douglas, S.M.3    Wu, B.4    Echols, N.5    Smith, A.6    Milburn, D.7    Montelione, G.T.8    Zhao, H.9    Gerstein, M.10
  • 38
    • 1442336002 scopus 로고    scopus 로고
    • PSI-phase 1 and beyond
    • Editorial
    • Editorial: PSI-phase 1 and beyond. Nat Struct Mol Biol 2004, 11:201.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 201
  • 39
    • 0141815541 scopus 로고    scopus 로고
    • Analysis of singleton ORFans in fully sequenced microbial genomes
    • A second biggest open question in structural genomics and fold recognition: what are these sequences?
    • Siew N., Fischer D. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins. 53:2003;241-251 A second biggest open question in structural genomics and fold recognition: what are these sequences?
    • (2003) Proteins , vol.53 , pp. 241-251
    • Siew, N.1    Fischer, D.2
  • 40
    • 0345373988 scopus 로고    scopus 로고
    • XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators
    • Luz J.G., Hassig C.A., Pickle C., Godzik A., Meyer B.J., Wilson I.A. XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. Genes Dev. 17:2003;977-990
    • (2003) Genes Dev , vol.17 , pp. 977-990
    • Luz, J.G.1    Hassig, C.A.2    Pickle, C.3    Godzik, A.4    Meyer, B.J.5    Wilson, I.A.6
  • 44
    • 0037197857 scopus 로고    scopus 로고
    • Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome
    • Kihara D., Zhang Y., Lu H., Kolinski A., Skolnick J. Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci USA. 99:2002;5993-5998
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5993-5998
    • Kihara, D.1    Zhang, Y.2    Lu, H.3    Kolinski, A.4    Skolnick, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.