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Volumn 79, Issue 7, 2011, Pages 2086-2096

Analysis of protein function and its prediction from amino acid sequence

Author keywords

Gene ontology; Neural network; Prediction; Protein function; Protein function transfer

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DATA BASE; MOLECULAR GENETICS; NERVE CELL NETWORK; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN TRANSPORT; SEQUENCE ANALYSIS;

EID: 79958759599     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23029     Document Type: Article
Times cited : (117)

References (63)
  • 2
    • 0345186060 scopus 로고    scopus 로고
    • Infering function from structure
    • Bourne PE, Weissig H, editors. Hoboken, NJ: Wiley-Liss;
    • Bartlett G, Todd A, Thornton J. Infering function from structure. In: Bourne PE, Weissig H, editors. Structural bioinformatics: Hoboken, NJ: Wiley-Liss; 2003.
    • (2003) Structural bioinformatics
    • Bartlett, G.1    Todd, A.2    Thornton, J.3
  • 3
    • 70349705654 scopus 로고    scopus 로고
    • Influence of sequence changes and environment on intrinsically disordered proteins
    • Mohan A, Uversky VN, Radivojac P. Influence of sequence changes and environment on intrinsically disordered proteins. PLoS Comput Biol 2009; 5: e1000497.
    • (2009) PLoS Comput Biol , vol.5
    • Mohan, A.1    Uversky, V.N.2    Radivojac, P.3
  • 4
    • 0003450992 scopus 로고
    • NC-IUBMB) NCotIUoBaMB. New York: Academic Press;
    • (NC-IUBMB) NCotIUoBaMB. Enzyme nomenclature. New York: Academic Press; 1992.
    • (1992) Enzyme nomenclature
  • 7
    • 77953936166 scopus 로고    scopus 로고
    • The human phenotype ontology
    • Robinson PN, Mundlos S. The human phenotype ontology. Clin Genet 2010; 77: 525-534.
    • (2010) Clin Genet , vol.77 , pp. 525-534
    • Robinson, P.N.1    Mundlos, S.2
  • 8
    • 0345863927 scopus 로고    scopus 로고
    • The Unified Medical Language System (UMLS): integrating biomedical terminology
    • Database issue
    • Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 2004; 32 (Database issue): D267-D270.
    • (2004) Nucleic Acids Res , vol.32
    • Bodenreider, O.1
  • 10
    • 38549144166 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
    • Database issue
    • Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36 (Database issue): D475-D479.
    • (2008) Nucleic Acids Res , vol.36
    • Liolios, K.1    Mavromatis, K.2    Tavernarakis, N.3    Kyrpides, N.C.4
  • 13
    • 0037460964 scopus 로고    scopus 로고
    • Prediction of human protein function according to gene ontology categories
    • Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to gene ontology categories. Bioinformatics 2003; 19: 635-642.
    • (2003) Bioinformatics , vol.19 , pp. 635-642
    • Jensen, L.J.1    Gupta, R.2    Staerfeldt, H.H.3    Brunak, S.4
  • 17
    • 13244268370 scopus 로고    scopus 로고
    • GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
    • Martin DM, Berriman M, Barton GJ. GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 2004; 5: 178.
    • (2004) BMC Bioinformatics , vol.5 , pp. 178
    • Martin, D.M.1    Berriman, M.2    Barton, G.J.3
  • 18
    • 33744471931 scopus 로고    scopus 로고
    • Enhanced automated function prediction using distantly related sequences and contextual association by PFP
    • Hawkins T, Luban S, Kihara D. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 2006; 15: 1550-1556.
    • (2006) Protein Sci , vol.15 , pp. 1550-1556
    • Hawkins, T.1    Luban, S.2    Kihara, D.3
  • 20
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003; 21: 697-700.
    • (2003) Nat Biotechnol , vol.21 , pp. 697-700
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 21
    • 0742304254 scopus 로고    scopus 로고
    • Prediction of protein function using protein-protein interaction data
    • Deng M, Zhang K, Mehta S, Chen T, Sun F. Prediction of protein function using protein-protein interaction data. J Comput Biol 2003; 10: 947-960.
    • (2003) J Comput Biol , vol.10 , pp. 947-960
    • Deng, M.1    Zhang, K.2    Mehta, S.3    Chen, T.4    Sun, F.5
  • 22
    • 1542271409 scopus 로고    scopus 로고
    • Predicting protein function from protein/protein interaction data: a probabilistic approach
    • Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 2003; 19 (Suppl 1): i197-i204.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Letovsky, S.1    Kasif, S.2
  • 23
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci USA 2003; 100: 8348-8353.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.5
  • 24
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science 2004; 306: 1555-1558.
    • (2004) Science , vol.306 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 25
    • 6944227836 scopus 로고    scopus 로고
    • Automated prediction of protein function and detection of functional sites from structure
    • Pazos F, Sternberg MJ. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci USA 2004; 101: 14754-14759.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14754-14759
    • Pazos, F.1    Sternberg, M.J.2
  • 26
    • 11844292002 scopus 로고    scopus 로고
    • Inference of protein function from protein structure
    • Pal D, Eisenberg D. Inference of protein function from protein structure. Structure 2005; 13: 121-130.
    • (2005) Structure , vol.13 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 27
    • 29144442904 scopus 로고    scopus 로고
    • Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
    • Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 2005; 21 (Suppl 1): i302-i310.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Nabieva, E.1    Jim, K.2    Agarwal, A.3    Chazelle, B.4    Singh, M.5
  • 30
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • Devos D, Valencia A. Practical limits of function prediction. Proteins 2000; 41: 98-107.
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 31
    • 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 CA, 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.
    • (2000) J Mol Biol , vol.297 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 32
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001; 307: 1113-1143.
    • (2001) J Mol Biol , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 33
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • Tian W, Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 2003; 333: 863-882.
    • (2003) J Mol Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 34
    • 61649112657 scopus 로고    scopus 로고
    • Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer
    • Addou S, Rentzsch R, Lee D, Orengo CA. Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer. J Mol Biol 2009; 387: 416-430.
    • (2009) J Mol Biol , vol.387 , pp. 416-430
    • Addou, S.1    Rentzsch, R.2    Lee, D.3    Orengo, C.A.4
  • 35
    • 40749111548 scopus 로고    scopus 로고
    • ConFunc-functional annotation in the twilight zone
    • Wass MN, Sternberg MJ. ConFunc-functional annotation in the twilight zone. Bioinformatics 2008; 24: 798-806.
    • (2008) Bioinformatics , vol.24 , pp. 798-806
    • Wass, M.N.1    Sternberg, M.J.2
  • 37
    • 77951518446 scopus 로고    scopus 로고
    • Hierarchical classification of gene ontology terms using the GOstruct method
    • Sokolov A, Ben-Hur A. Hierarchical classification of gene ontology terms using the GOstruct method. J Bioinform Comput Biol 2010; 8: 357-376.
    • (2010) J Bioinform Comput Biol , vol.8 , pp. 357-376
    • Sokolov, A.1    Ben-Hur, A.2
  • 38
    • 0031976258 scopus 로고    scopus 로고
    • Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis
    • Eisen JA. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 1998; 8: 163-167.
    • (1998) Genome Res , vol.8 , pp. 163-167
    • Eisen, J.A.1
  • 39
    • 33745630672 scopus 로고    scopus 로고
    • Functional classification using phylogenomic inference
    • Brown D, Sjolander K. Functional classification using phylogenomic inference. PLoS Comput Biol 2006; 2: e77.
    • (2006) PLoS Comput Biol , vol.2
    • Brown, D.1    Sjolander, K.2
  • 40
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm M, Storm CE, Sonnhammer EL. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 2001; 314: 1041-1052.
    • (2001) J Mol Biol , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 41
    • 33748776559 scopus 로고    scopus 로고
    • Automated protein function prediction-the genomic challenge
    • Friedberg I. Automated protein function prediction-the genomic challenge. Brief Bioinform 2006; 7: 225-242.
    • (2006) Brief Bioinform , vol.7 , pp. 225-242
    • Friedberg, I.1
  • 42
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee D, Redfern O, Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007; 8: 995-1005.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 43
    • 55449125498 scopus 로고    scopus 로고
    • The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function
    • Punta M, Ofran Y. The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol 2008; 4: e1000160.
    • (2008) PLoS Comput Biol , vol.4
    • Punta, M.1    Ofran, Y.2
  • 44
    • 38349144394 scopus 로고    scopus 로고
    • Understanding the molecular machinery of genetics through 3D structures
    • Laskowski RA, Thornton JM. Understanding the molecular machinery of genetics through 3D structures. Nat Rev Genet 2008; 9: 141-151.
    • (2008) Nat Rev Genet , vol.9 , pp. 141-151
    • Laskowski, R.A.1    Thornton, J.M.2
  • 45
    • 36349010138 scopus 로고    scopus 로고
    • Protein interactions and disease: computational approaches to uncover the etiology of diseases
    • Kann MG. Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 2007; 8: 333-346.
    • (2007) Brief Bioinform , vol.8 , pp. 333-346
    • Kann, M.G.1
  • 47
    • 62549146620 scopus 로고    scopus 로고
    • Protein function prediction-the power of multiplicity
    • Rentzsch R, Orengo CA. Protein function prediction-the power of multiplicity. Trends Biotechnol 2009; 27: 210-219.
    • (2009) Trends Biotechnol , vol.27 , pp. 210-219
    • Rentzsch, R.1    Orengo, C.A.2
  • 48
    • 0033048066 scopus 로고    scopus 로고
    • Moonlighting proteins
    • Jeffery CJ. Moonlighting proteins. Trends Biochem Sci 1999; 24: 8-11.
    • (1999) Trends Biochem Sci , vol.24 , pp. 8-11
    • Jeffery, C.J.1
  • 49
    • 62949096122 scopus 로고    scopus 로고
    • Moonlighting proteins-an update
    • Jeffery CJ. Moonlighting proteins-an update. Mol Biosyst 2009; 5: 345-350.
    • (2009) Mol Biosyst , vol.5 , pp. 345-350
    • Jeffery, C.J.1
  • 50
    • 9944225262 scopus 로고    scopus 로고
    • Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins
    • Jeffery CJ. Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins. Curr Opin Struct Biol 2004; 14: 663-668.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 663-668
    • Jeffery, C.J.1
  • 52
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner SE. Errors in genome annotation. Trends Genet 1999; 15: 132-133.
    • (1999) Trends Genet , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 53
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    • Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 2009; 5: e1000605.
    • (2009) PLoS Comput Biol , vol.5
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 54
    • 65449147869 scopus 로고    scopus 로고
    • The use of gene ontology evidence codes in preventing classifier assessment bias
    • Rogers MF, Ben-Hur A. The use of gene ontology evidence codes in preventing classifier assessment bias. Bioinformatics 2009; 25: 1173-1177.
    • (2009) Bioinformatics , vol.25 , pp. 1173-1177
    • Rogers, M.F.1    Ben-Hur, A.2
  • 55
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999; 12: 85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 56
    • 33746622998 scopus 로고    scopus 로고
    • Protein-protein interactions more conserved within species than across species
    • Mika S, Rost B. Protein-protein interactions more conserved within species than across species. PLoS Comput Biol 2006; 2: e79.
    • (2006) PLoS Comput Biol , vol.2
    • Mika, S.1    Rost, B.2
  • 57
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill KA. Polymer principles and protein folding. Protein Sci 1999; 8: 1166-1180.
    • (1999) Protein Sci , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 59
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005; 6: 197-208.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 61
    • 33744471138 scopus 로고    scopus 로고
    • New avenues in protein function prediction
    • Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci 2006; 15: 1527-1529.
    • (2006) Protein Sci , vol.15 , pp. 1527-1529
    • Friedberg, I.1    Jambon, M.2    Godzik, A.3
  • 62
    • 36749082814 scopus 로고    scopus 로고
    • Assessment of intramolecular contact predictions for CASP7
    • Izarzugaza JM, Grana O, Tress ML, Valencia A, Clarke ND. Assessment of intramolecular contact predictions for CASP7. Proteins 2007; 69 (Suppl 8): 152-158.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 152-158
    • Izarzugaza, J.M.1    Grana, O.2    Tress, M.L.3    Valencia, A.4    Clarke, N.D.5
  • 63
    • 84943274699 scopus 로고
    • A direct adaptive method for faster backpropagation learning: the RPROP algorithm
    • Riedmiller M, Braun H. A direct adaptive method for faster backpropagation learning: the RPROP algorithm. Proc IEEE Int Conf Neural Netw 1993; 1: 586-591.
    • (1993) Proc IEEE Int Conf Neural Netw , vol.1 , pp. 586-591
    • Riedmiller, M.1    Braun, H.2


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