메뉴 건너뛰기




Volumn 64, Issue 19-20, 2007, Pages 2505-2511

Computational protein function prediction: Are we making progress?

Author keywords

AFP; Aspartate dehydrogenase; Aspartate oxidase; Bioinformatics; CASP; NAD synthesis; Non orthologous replacement; Protein function prediction

Indexed keywords

ASPARTATE OXIDASE; NICOTINAMIDE ADENINE DINUCLEOTIDE;

EID: 35648948885     PISSN: 1420682X     EISSN: 15691632     Source Type: Journal    
DOI: 10.1007/s00018-007-7211-y     Document Type: Short Survey
Times cited : (50)

References (30)
  • 1
    • 23944495106 scopus 로고    scopus 로고
    • Metagenomics for studying unculturable microorganisms: Cutting the Gordian knot
    • Schloss, P. D. and Handelsman, J. (2005) Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 6, 229.
    • (2005) Genome Biol , vol.6 , pp. 229
    • Schloss, P.D.1    Handelsman, J.2
  • 3
    • 26944480402 scopus 로고    scopus 로고
    • Beyond annotation transfer by homology: Novel protein-function prediction methods to assist drug discovery
    • Ofran, Y., Punta, M., Schneider, R. and Rost, B. (2005) Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discovery Today 10, 1475-1482.
    • (2005) Drug Discovery Today , vol.10 , pp. 1475-1482
    • Ofran, Y.1    Punta, M.2    Schneider, R.3    Rost, B.4
  • 4
    • 33748776559 scopus 로고    scopus 로고
    • Automated protein function prediction - the genomic challenge
    • Friedberg, I. (2006) Automated protein function prediction - the genomic challenge. Brief. Bioinform. 7, 225-242.
    • (2006) Brief. Bioinform , vol.7 , pp. 225-242
    • Friedberg, I.1
  • 5
    • 0027133165 scopus 로고
    • Functions of the gene products of Escherichia coli
    • Riley, M. (1993) Functions of the gene products of Escherichia coli. Microbiol. Rev. 57, 862-952.
    • (1993) Microbiol. Rev , vol.57 , pp. 862-952
    • Riley, M.1
  • 7
    • 27744495232 scopus 로고    scopus 로고
    • Get ready to GO! A biologist's guide to the Gene Ontology
    • Lomax, J. (2005) Get ready to GO! A biologist's guide to the Gene Ontology. Brief. Bioinform. 6, 298-304.
    • (2005) Brief. Bioinform , vol.6 , pp. 298-304
    • Lomax, J.1
  • 8
    • 30344440806 scopus 로고    scopus 로고
    • The prediction of protein function at CASP6
    • Soro, S. and Tramontano, A. (2005) The prediction of protein function at CASP6. Proteins 61 Suppl. 7, 201-213.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 201-213
    • Soro, S.1    Tramontano, A.2
  • 15
    • 3242888755 scopus 로고    scopus 로고
    • Annotation of bacterial genomes using improved phylogenomic profiles
    • Enault, F., Suhre, K., Abergel, C., Poirot, O. and Claverie, J. M. (2003) Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics 19 Suppl 1, i105-i107.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Enault, F.1    Suhre, K.2    Abergel, C.3    Poirot, O.4    Claverie, J.M.5
  • 17
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • Watson, J. D., Laskowski, R. A. and Thornton, J. M. (2005) Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol. 15, 275-284.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 275-284
    • Watson, J.D.1    Laskowski, R.A.2    Thornton, J.M.3
  • 18
    • 0037480738 scopus 로고    scopus 로고
    • Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation
    • Lord, P. W., Stevens, R. D., Brass, A. and Goble, C. A. (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19, 1275-1283.
    • (2003) Bioinformatics , vol.19 , pp. 1275-1283
    • Lord, P.W.1    Stevens, R.D.2    Brass, A.3    Goble, C.A.4
  • 19
    • 33748335463 scopus 로고    scopus 로고
    • A new measure for functional similarity of gene products based on Gene Ontology
    • Schlicker, A., Domingues, F. S., Rahnenfuhrer, J. and Lengauer, T. (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 7, 302.
    • (2006) BMC Bioinformatics , vol.7 , pp. 302
    • Schlicker, A.1    Domingues, F.S.2    Rahnenfuhrer, J.3    Lengauer, T.4
  • 20
    • 34447294237 scopus 로고    scopus 로고
    • A new method to measure the semantic similarity of GO terms
    • Wang, J. Z., Du, Z., Payattakool, R., Yu, P. S. and Chen, C. F. (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23, 1274-1281.
    • (2007) Bioinformatics , vol.23 , pp. 1274-1281
    • Wang, J.Z.1    Du, Z.2    Payattakool, R.3    Yu, P.S.4    Chen, C.F.5
  • 21
    • 0034776419 scopus 로고    scopus 로고
    • Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT
    • Kretschmann, E., Fleischmann, W. and Apweiler, R. (2001) Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics 17, 920-926.
    • (2001) Bioinformatics , vol.17 , pp. 920-926
    • Kretschmann, E.1    Fleischmann, W.2    Apweiler, R.3
  • 23
    • 33744471931 scopus 로고    scopus 로고
    • Enhanced automated function prediction using distantly related sequences and contextual association by PFP
    • Hawkins, T., Luban, S. and Kihara, D. (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci. 15, 1550-1556.
    • (2006) Protein Sci , vol.15 , pp. 1550-1556
    • Hawkins, T.1    Luban, S.2    Kihara, D.3
  • 24
    • 27644434408 scopus 로고    scopus 로고
    • Phydbac "Gene Function Predictor": A gene annotation tool based on genomic context analysis
    • Enault, F., Suhre, K. and Claverie, J.-M. (2005) Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics 6, 247.
    • (2005) BMC Bioinformatics , vol.6 , pp. 247
    • Enault, F.1    Suhre, K.2    Claverie, J.-M.3
  • 25
    • 11844292002 scopus 로고    scopus 로고
    • Inference of protein function from protein structure
    • Pal, D. and Eisenberg, D. (2005) Inference of protein function from protein structure. Structure (Camb) 13, 121-130.
    • (2005) Structure (Camb) , vol.13 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 26
    • 13444261288 scopus 로고    scopus 로고
    • PA-GOSUB: A searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
    • Lu, P., Szafron, D., Greiner, R., Wishart, D. S., Fyshe, A., Pearcy, B., Poulin, B., Eisner, R., Ngo, D. and Lamb, N. (2005) PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. Nucleic Acids Res. 33, D147-D153.
    • (2005) Nucleic Acids Res , vol.33
    • Lu, P.1    Szafron, D.2    Greiner, R.3    Wishart, D.S.4    Fyshe, A.5    Pearcy, B.6    Poulin, B.7    Eisner, R.8    Ngo, D.9    Lamb, N.10
  • 29
    • 0037424378 scopus 로고    scopus 로고
    • Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643
    • Yang, Z., Savchenko, A., Yakunin, A., Zhang, R., Edwards, A., Arrowsmith, C. and Tong, L. (2003) Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643. J. Biol. Chem. 278, 8804-8808.
    • (2003) J. Biol. Chem , vol.278 , pp. 8804-8808
    • Yang, Z.1    Savchenko, A.2    Yakunin, A.3    Zhang, R.4    Edwards, A.5    Arrowsmith, C.6    Tong, L.7
  • 30
    • 33745190979 scopus 로고    scopus 로고
    • Revisiting the prediction of protein function at CASP6
    • Pellegrini-Calace, M., Soro, S. and Tramontano, A. (2006) Revisiting the prediction of protein function at CASP6. FEBS J. 273, 2977-2983.
    • (2006) FEBS J , vol.273 , pp. 2977-2983
    • Pellegrini-Calace, M.1    Soro, S.2    Tramontano, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.