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Volumn 8, Issue 9, 2009, Pages 4362-4371

The Bologna annotation resource: A non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis

Author keywords

Alignment coverage; Cross genome comparison; Grid technology; Protein functional annotation

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; COMPARATIVE STUDY; CONTROLLED STUDY; EUKARYOTE; GENE MAPPING; GENE SEQUENCE; GENOME; GENOME ANALYSIS; HEALTH CARE ORGANIZATION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FUNCTION; PROTEIN TRANSPORT;

EID: 70349906952     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900204r     Document Type: Article
Times cited : (10)

References (35)
  • 1
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C.; Lesk, A. M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986, 5 (4), 823-826.
    • (1986) EMBO J. , vol.5 , Issue.4 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 2
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • DOI 10.1006/jmbi.1993.1489
    • Holm, L.; Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 1993, 233, 123-138. (Pubitemid 23288916)
    • (1993) Journal of Molecular Biology , vol.233 , Issue.1 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 3
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1998, 11, 739-747.
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 4
    • 36949008379 scopus 로고    scopus 로고
    • CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures
    • Redfern, O.; Harrison, A.; Dallman, T.; Pearl, F. M. G.; Orengo, C. CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLOS Comput. Biol. 2007, 3, e232.
    • (2007) PLOS Comput. Biol. , vol.3
    • Redfern, O.1    Harrison, A.2    Dallman, T.3    Pearl, F.M.G.4    Orengo, C.5
  • 5
    • 33746962182 scopus 로고    scopus 로고
    • EVEREST: Automatic identification and classification of protein domains in all protein sequences
    • Portugaly, E.; Harel, A.; Linial, N.; Linial, M. EVEREST: automatic identification and classification of protein domains in all protein sequences. BMC Bioinf. 2006, 7, 277.
    • (2006) BMC Bioinf. , vol.7 , pp. 277
    • Portugaly, E.1    Harel, A.2    Linial, N.3    Linial, M.4
  • 7
    • 33846057724 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence data base of genomes, transcripts and proteins
    • Pruitt, K. D.; Tatusova, T.; Maglott, D. R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence data base of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35, D61-5.
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 10
    • 0034677669 scopus 로고    scopus 로고
    • Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
    • DOI 10.1006/jmbi.2000.3550
    • Wilson, C. A.; Kreychman, J.; Gerstein, M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 2000, 297, 233-249. (Pubitemid 30695553)
    • (2000) Journal of Molecular Biology , vol.297 , Issue.1 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 11
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • DOI 10.1016/S0022-2836(02)00016-5
    • Rost, B. Enzyme function less conserved than anticipated. J. Mol. Biol. 2002, 318, 595-608. (Pubitemid 34734850)
    • (2002) Journal of Molecular Biology , vol.318 , Issue.2 , pp. 595-608
    • Rost, B.1
  • 12
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • DOI 10.1016/j.jmb.2003.08.057
    • Tian, W.; Skolnick, J. How well is enzyme function conserved as a function of pairwise sequence identity. J. Mol. Biol. 2002, 333, 863-882. (Pubitemid 37268023)
    • (2003) Journal of Molecular Biology , vol.333 , Issue.4 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 13
    • 0033985049 scopus 로고    scopus 로고
    • The SYSTERS protein sequence cluster set
    • Krause, A.; Stoye, J.; Vingron, M. The SYSTERS protein sequence cluster set. Nucleic Acids Res. 2002, 28, 270-272. (Pubitemid 30047777)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 270-272
    • Krause, A.1    Stoye, J.2    Vingron, M.3
  • 14
    • 0035070578 scopus 로고    scopus 로고
    • Picasso: Generating a covering set of protein family profiles
    • Hedger, A.; Holm, L. Picasso: generating a covering set of protein family profiles. Bioinformatics 2001, 17, 272-279.
    • (2001) Bioinformatics , vol.17 , pp. 272-279
    • Hedger, A.1    Holm, L.2
  • 15
    • 0035167151 scopus 로고    scopus 로고
    • The iProClass integrated data base for protein functional analysis
    • Wu, C. H.; Huang, H.; Nikolskaya, A.; Hu, Z.; Barker, W. C. The iProClass integrated data base for protein functional analysis. Nucleic Acids Res. 2001, 29, 52-54.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 52-54
    • Wu, C.H.1    Huang, H.2    Nikolskaya, A.3    Hu, Z.4    Barker, W.C.5
  • 17
    • 24644474560 scopus 로고    scopus 로고
    • The predictive power of the CluSTr database
    • DOI 10.1093/bioinformatics/bti542
    • Petryszak, R.; Kretschmann, E.; Wieser, D.; Apweiler, R. The predictive power of the CluSTr data base. Bioinformatics 2005, 3604-3609. (Pubitemid 41264094)
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3604-3609
    • Petryszak, R.1    Kretschmann, E.2    Wieser, D.3    Apweiler, R.4
  • 19
    • 46249133773 scopus 로고    scopus 로고
    • Efficient algorithms for accurate hierarchical clustering of huge datasets: Tackling the entire protein space
    • DOI 10.1093/bioinformatics/btn174
    • Loewenstein, Y.; Portugaly, E.; Fromer, M.; Linial, M. Efficient algorithms for accurate hierarchical clustering of huge data sets: tackling the entire protein space. Bioinformatics 2008, 24, i41-i49. (Pubitemid 351911656)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Loewenstein, Y.1    Portugaly, E.2    Fromer, M.3    Linial, M.4
  • 20
    • 70349335150 scopus 로고    scopus 로고
    • Wiley-IEEE Press: Hoboken, NJ
    • Xu, R.; Wunsch, D. Clustering; Wiley-IEEE Press: Hoboken, NJ, 2009.
    • (2009) Clustering
    • Xu, R.1    Wunsch, D.2
  • 22
    • 25444502317 scopus 로고    scopus 로고
    • JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
    • Sperisen, P.; Pagni, M. JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture. BMC Bioinf. 2005, 6, 216.
    • (2005) BMC Bioinf. , vol.6 , pp. 216
    • Sperisen, P.1    Pagni, M.2
  • 23
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A. J.; Van Dongen, S.; Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30, 1575-1584. (Pubitemid 34679732)
    • (2002) Nucleic Acids Research , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 24
    • 0034767547 scopus 로고    scopus 로고
    • Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins
    • DOI 10.1101/gr. 183801
    • Hegyi, H.; Gerstein, M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 2001, 11, 1632-1640. (Pubitemid 33040490)
    • (2001) Genome Research , vol.11 , Issue.10 , pp. 1632-1640
    • Hegyi, H.1    Gerstein, M.2
  • 27
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch, A.; Apweiler, R. The SWISS-PROT protein sequence data base and its supplement TrEMBL. Nucleic Acids Res. 2000, 28, 45-48. (Pubitemid 30047711)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 29
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nat. Genet. 2000, 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
  • 31
    • 33645323768 scopus 로고    scopus 로고
    • Hierarchical multi-label prediction of gene function
    • Barutcuoglu, Z.; Schapire, R. E.; Troyanskaya, O. G. Hierarchical multi-label prediction of gene function. Bioinformatics 2006, 22 (7), 830-836.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 830-836
    • Barutcuoglu, Z.1    Schapire, R.E.2    Troyanskaya, O.G.3
  • 33
    • 28444456164 scopus 로고    scopus 로고
    • Good Lower and Upper Bounds on Binomial Coefficients
    • Stanica, P. Good Lower and Upper Bounds on Binomial Coefficients. JIPAM 2001, 2 (3), 30.
    • (2001) JIPAM , vol.2 , Issue.3 , pp. 30
    • Stanica, P.1
  • 35
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins data base for the investigation of sequences and structures
    • Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins data base for the investigation of sequences and structures. J. Mol. Biol. 1995, 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.