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Volumn 17, Issue 1, 2010, Pages 55-72

Graphlet kernels for prediction of functional residues in protein structures

Author keywords

Algorithms; Graphs; Kernel methods; Machine learning; Protein function; Protein structure

Indexed keywords

PROTEIN; PROTEIN KINASE LCK;

EID: 77149167608     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0029     Document Type: Article
Times cited : (49)

References (101)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F., Madden, T.L., Schaffer, A.A., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 2
    • 0027967593 scopus 로고
    • A graph-theoretic approach to the identification of threedimensional patterns of amino acid side-chains in protein structures
    • Artymiuk, P.J., Poirrette, A.R., Grindley, H.M., et al. 1994. A graph-theoretic approach to the identification of threedimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol. 243, 327-344.
    • (1994) J. Mol. Biol. , vol.243 , pp. 327-344
    • Artymiuk, P.J.1    Poirrette, A.R.2    Grindley, H.M.3
  • 3
    • 0346057951 scopus 로고    scopus 로고
    • Small-world communication of residues and significance for protein dynamics
    • Atilgan, A.R., Akan, P., and Baysal, C. 2004. Small-world communication of residues and significance for protein dynamics. Biophys. J. 86, 85-91.
    • (2004) Biophys. J. , vol.86 , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 4
    • 0028950817 scopus 로고
    • Characterizing the microenvironment surrounding protein sites
    • Bagley, S.C., and Altman, R.B. 1995. Characterizing the microenvironment surrounding protein sites. Protein Sci. 4, 622-635.
    • (1995) Protein Sci. , vol.4 , pp. 622-635
    • Bagley, S.C.1    Altman, R.B.2
  • 5
    • 13444273448 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • Bairoch, A., Apweiler, R., Wu, C.H., et al. 2005. The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, Database Issue, D154-D159.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.DATABASE ISSUE
    • Bairoch, A.1    Apweiler, R.2    Wu, C.H.3
  • 6
    • 8844272471 scopus 로고    scopus 로고
    • Phosphoproteomic analysis of the developing mouse brain
    • Ballif, B.A., Villen, J., Beausoleil, S.A., et al. 2004. Phosphoproteomic analysis of the developing mouse brain. Mol. Cell Proteomics 3, 1093-1101.
    • (2004) Mol. Cell Proteomics , vol.3 , pp. 1093-1101
    • Ballif, B.A.1    Villen, J.2    Beausoleil, S.A.3
  • 7
    • 33744491290 scopus 로고    scopus 로고
    • Structure-based function inference using protein family-specific fingerprints
    • Bandyopadhyay, D., Huan, J., Liu, J., et al. 2006. Structure-based function inference using protein family-specific fingerprints. Protein Sci. 15, 1537-1543.
    • (2006) Protein Sci. , vol.15 , pp. 1537-1543
    • Bandyopadhyay, D.1    Huan, J.2    Liu, J.3
  • 9
    • 0033757806 scopus 로고    scopus 로고
    • The protein data bank and the challenge of structural genomics
    • Berman, H., Bhat, T.N., Bourne, P., et al. 2000. The protein data bank and the challenge of structural genomics. Nat. Struct. Biol. 7, 957-959.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 957-959
    • Berman, H.1    Bhat, T.N.2    Bourne, P.3
  • 10
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom, N., Gammeltoft, S., and Brunak, S. 1999. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294, 1351-1362.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 11
    • 33745771638 scopus 로고    scopus 로고
    • Protein function prediction via graph kernels
    • Borgwardt, K.M., Ong, C.S., Schonauer, S., et al. 2005. Protein function prediction via graph kernels. Bioinformatics 21, Suppl 1, i47-i56.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Borgwardt, K.M.1    Ong, C.S.2    Schonauer, S.3
  • 12
    • 0036093538 scopus 로고    scopus 로고
    • Analysis of homodimeric protein interfaces by graph-spectral methods
    • Brinda, K.V., Kannan, N., and Vishveshwara, S. 2002. Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Eng. 15, 265-277.
    • (2002) Protein Eng. , vol.15 , pp. 265-277
    • Brinda, K.V.1    Kannan, N.2    Vishveshwara, S.3
  • 13
    • 0037422596 scopus 로고    scopus 로고
    • Structural basis and prediction of substrate specificity in protein serine=threonine kinases
    • Brinkworth, R.I., Breinl, R.A., and Kobe, B. 2003. Structural basis and prediction of substrate specificity in protein serine=threonine kinases. Proc. Natl. Acad. Sci. U.S.A. 100, 74-79.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 74-79
    • Brinkworth, R.I.1    Breinl, R.A.2    Kobe, B.3
  • 14
    • 0032831070 scopus 로고    scopus 로고
    • Structural genomics: Beyond the human genome project
    • Burley, S.K., Almo, S.C., Bonanno, J.B., et al. 1999. Structural genomics: beyond the human genome project. Nat. Genet. 23, 151-157.
    • (1999) Nat. Genet. , vol.23 , pp. 151-157
    • Burley, S.K.1    Almo, S.C.2    Bonanno, J.B.3
  • 16
    • 47849089500 scopus 로고    scopus 로고
    • Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder
    • Collins, M.O., Yu, L., Campuzano, I., et al. 2008. Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder. Mol. Cell Proteomics 7, 1331-1348.
    • (2008) Mol. Cell Proteomics , vol.7 , pp. 1331-1348
    • Collins, M.O.1    Yu, L.2    Campuzano, I.3
  • 17
    • 42949160024 scopus 로고    scopus 로고
    • From protein-disease associations to disease informatics
    • Dalkilic, M.M., Costello, J.C., Clark, W.T., et al. 2008. From protein-disease associations to disease informatics. Front. Biosci. 13, 3391-3407.
    • (2008) Front. Biosci. , vol.13 , pp. 3391-3407
    • Dalkilic, M.M.1    Costello, J.C.2    Clark, W.T.3
  • 18
    • 13244289881 scopus 로고    scopus 로고
    • Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins
    • Diella, F., Cameron, S., Gemund, C., et al. 2004. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinform. 5, 79.
    • (2004) BMC Bioinform. , vol.5 , pp. 79
    • Diella, F.1    Cameron, S.2    Gemund, C.3
  • 19
    • 0035961329 scopus 로고    scopus 로고
    • The structural basis of protein folding and its links with human disease
    • Dobson, C.M. 2001. The structural basis of protein folding and its links with human disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356, 133-145.
    • (2001) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.356 , pp. 133-145
    • Dobson, C.M.1
  • 21
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock, A.H. 2001. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312, 885-896.
    • (2001) J. Mol. Biol. , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 22
    • 34548736602 scopus 로고    scopus 로고
    • Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin
    • Espinoza-Fonseca, L.M., Kast, D. and Thomas, D.D. 2007. Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin. Biophys. J. 93, 2083-2090.
    • (2007) Biophys. J. , vol.93 , pp. 2083-2090
    • Espinoza-Fonseca, L.M.1    Kast, D.2    Thomas, D.D.3
  • 23
    • 51949096545 scopus 로고    scopus 로고
    • Thermodynamic and structural basis of phosphorylationinduced disorder-to-order transition in the regulatory light chain of smooth muscle myosin
    • Espinoza-Fonseca, L.M., Kast, D. and Thomas, D.D. 2008. Thermodynamic and structural basis of phosphorylationinduced disorder-to-order transition in the regulatory light chain of smooth muscle myosin. J. Am. Chem. Soc. 130, 12208-12209.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 12208-12209
    • Espinoza-Fonseca, L.M.1    Kast, D.2    Thomas, D.D.3
  • 24
    • 0032483312 scopus 로고    scopus 로고
    • Method for prediction of protein function from sequence using the sequence-tostructure-to-function paradigm with application to glutaredoxins=thioredoxins and T1 ribonucleases
    • Fetrow, J.S., and Skolnick, J. 1998. Method for prediction of protein function from sequence using the sequence-tostructure-to-function paradigm with application to glutaredoxins=thioredoxins and T1 ribonucleases. J. Mol. Biol. 281, 949-968.
    • (1998) J. Mol. Biol. , vol.281 , pp. 949-968
    • Fetrow, J.S.1    Skolnick, J.2
  • 25
    • 0036198435 scopus 로고    scopus 로고
    • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
    • Ficarro, S.B., McCleland, M.L., Stukenberg, P.T., et al. 2002. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20, 301-305.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 301-305
    • Ficarro, S.B.1    McCleland, M.L.2    Stukenberg, P.T.3
  • 26
    • 4644357300 scopus 로고    scopus 로고
    • Kinase peptide specificity: Improved determination and relevance to protein phosphorylation
    • Fujii, K., Zhu, G., Liu, Y., et al. 2004. Kinase peptide specificity: improved determination and relevance to protein phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 101, 13744-13749.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 13744-13749
    • Fujii, K.1    Zhu, G.2    Liu, Y.3
  • 28
    • 30144442036 scopus 로고    scopus 로고
    • A method for localizing ligand binding pockets in protein structures
    • Glaser, F., Morris, R.J., Najmanovich, R.J., et al. 2006. A method for localizing ligand binding pockets in protein structures. Proteins 62, 479-488.
    • (2006) Proteins , vol.62 , pp. 479-488
    • Glaser, F.1    Morris, R.J.2    Najmanovich, R.J.3
  • 29
    • 40549094379 scopus 로고    scopus 로고
    • Combining molecular dynamics and machine learning to improve protein function recognition
    • Glazer, D.S., Radmer, R.J., and Altman, R.B. 2008. Combining molecular dynamics and machine learning to improve protein function recognition. Pac. Symp. Biocomput. 332-343.
    • (2008) Pac. Symp. Biocomput. , pp. 332-343
    • Glazer, D.S.1    Radmer, R.J.2    Altman, R.B.3
  • 30
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
    • Gnad, F., Ren, S., Cox, J., et al. 2007. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol. 8, R250.
    • (2007) Genome Biol. , vol.8
    • Gnad, F.1    Ren, S.2    Cox, J.3
  • 31
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene, L.H., and Higman, V.A. 2003. Uncovering network systems within protein structures. J. Mol. Biol. 334, 781-791.
    • (2003) J. Mol. Biol. , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 32
    • 0027475029 scopus 로고
    • The prediction and characterization of metal binding sites in proteins
    • Gregory, D.S., Martin, A.C., Cheetham, J.C., et al. 1993. The prediction and characterization of metal binding sites in proteins. Protein Eng. 6, 29-35.
    • (1993) Protein Eng. , vol.6 , pp. 29-35
    • Gregory, D.S.1    Martin, A.C.2    Cheetham, J.C.3
  • 33
    • 0027511808 scopus 로고
    • Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm
    • Grindley, H.M., Artymiuk, P.J., Rice, D.W., et al. 1993. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
    • (1993) J. Mol. Biol. , vol.229 , pp. 707-721
    • Grindley, H.M.1    Artymiuk, P.J.2    Rice, D.W.3
  • 34
    • 33646266474 scopus 로고    scopus 로고
    • Conformational changes in protein loops and helices induced by post-translational phosphorylation
    • Groban, E.S., Narayanan, A., and Jacobson, M.P. 2006. Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput. Biol. 2, e32.
    • (2006) PLoS Comput. Biol. , vol.2
    • Groban, E.S.1    Narayanan, A.2    Jacobson, M.P.3
  • 35
    • 57149116929 scopus 로고    scopus 로고
    • Tight regulation of unstructured proteins: From transcript synthesis to protein degradation
    • Gsponer, J., Futschik, M.E., Teichmann, S.A., et al. 2008. Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322, 1365-1368.
    • (2008) Science , vol.322 , pp. 1365-1368
    • Gsponer, J.1    Futschik, M.E.2    Teichmann, S.A.3
  • 36
    • 35448961596 scopus 로고    scopus 로고
    • A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw
    • Hamelberg, D., Shen, T., and McCammon, J.A. 2007. A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proc. Natl. Acad. Sci. U.S.A. 104, 14947-14951.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 14947-14951
    • Hamelberg, D.1    Shen, T.2    McCammon, J.A.3
  • 38
    • 42649118768 scopus 로고    scopus 로고
    • Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR
    • Hegedus, T., Serohijos, A.W., Dokholyan, N.V., et al. 2008. Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. J. Mol. Biol. 378, 1052-1063.
    • (2008) J. Mol. Biol. , vol.378 , pp. 1052-1063
    • Hegedus, T.1    Serohijos, A.W.2    Dokholyan, N.V.3
  • 39
    • 34547939672 scopus 로고    scopus 로고
    • Structure-based activity prediction for an enzyme of unknown function
    • Hermann, J.C., Marti-Arbona, R., Fedorov, A.A., et al. 2007. Structure-based activity prediction for an enzyme of unknown function. Nature 448, 775-779.
    • (2007) Nature , vol.448 , pp. 775-779
    • Hermann, J.C.1    Marti-Arbona, R.2    Fedorov, A.A.3
  • 40
    • 4444320150 scopus 로고    scopus 로고
    • Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry
    • Hjerrild, M., Stensballe, A., Rasmussen, T.E., et al. 2004. Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J. Proteome Res. 3, 426-433.
    • (2004) J. Proteome Res. , vol.3 , pp. 426-433
    • Hjerrild, M.1    Stensballe, A.2    Rasmussen, T.E.3
  • 41
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U., and Sander, C. 1994. Enlarged representative set of protein structures. Protein Sci. 3, 522-524.
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 42
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L., and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 44
    • 34347326305 scopus 로고    scopus 로고
    • Ligand binding and circular permutation modify residue interaction network in DHFR
    • Hu, Z., Bowen, D., Southerland, W.M., et al. 2007. Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput. Biol. 3, e117.
    • (2007) PLoS Comput. Biol. , vol.3
    • Hu, Z.1    Bowen, D.2    Southerland, W.M.3
  • 45
    • 23844484183 scopus 로고    scopus 로고
    • Comparing graph representations of protein structure for mining family-specific residue-based packing motifs
    • Huan, J., Bandyopadhyay, D., Wang, W., et al. 2005. Comparing graph representations of protein structure for mining family-specific residue-based packing motifs. J. Comput. Biol. 12, 657-671.
    • (2005) J. Comput. Biol. , vol.12 , pp. 657-671
    • Huan, J.1    Bandyopadhyay, D.2    Wang, W.3
  • 46
    • 2342473198 scopus 로고    scopus 로고
    • The importance of intrinsic disorder for protein phosphorylation
    • Iakoucheva, L.M., Radivojac, P., Brown, C.J., et al. 2004. The importance of intrinsic disorder for protein phosphorylation, Nucleic Acids Res. 32, 1037-1049.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1037-1049
    • Iakoucheva, L.M.1    Radivojac, P.2    Brown, C.J.3
  • 47
    • 36749082814 scopus 로고    scopus 로고
    • Assessment of intramolecular contact predictions for CASP7
    • Izarzugaza, J.M., Grana, O., Tress, M.L., et al. 2007. Assessment of intramolecular contact predictions for CASP7. Proteins 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
  • 49
    • 0035413607 scopus 로고    scopus 로고
    • Structural basis for control by phosphorylation
    • Johnson, L.N., and Lewis, R.J. 2001. Structural basis for control by phosphorylation. Chem. Rev. 101, 2209-2242.
    • (2001) Chem. Rev. , vol.101 , pp. 2209-2242
    • Johnson, L.N.1    Lewis, R.J.2
  • 50
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and Sander, C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 51
    • 1642452921 scopus 로고    scopus 로고
    • Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families
    • Kalinina, O.V., Mironov, A.A., Gelfand, M.S., et al. 2004. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci. 13, 443-456.
    • (2004) Protein Sci. , vol.13 , pp. 443-456
    • Kalinina, O.V.1    Mironov, A.A.2    Gelfand, M.S.3
  • 53
    • 0028032838 scopus 로고
    • Structural determinants of substrate selection by the human insulin-receptor protein-tyrosine kinase
    • Keane, N.E., Chavanieu, A., Quirk, P.G., et al. 1994. Structural determinants of substrate selection by the human insulin-receptor protein-tyrosine kinase. Eur. J. Biochem. 226, 525-536.
    • (1994) Eur. J. Biochem. , vol.226 , pp. 525-536
    • Keane, N.E.1    Chavanieu, A.2    Quirk, P.G.3
  • 54
    • 33847768378 scopus 로고    scopus 로고
    • Similar binding sites and different partners: Implications to shared proteins in cellular pathways
    • Keskin, O., and Nussinov, R. 2007. Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure 15, 341-354.
    • (2007) Structure , vol.15 , pp. 341-354
    • Keskin, O.1    Nussinov, R.2
  • 55
    • 8844219516 scopus 로고    scopus 로고
    • Prediction of phosphorylation sites using SVMs
    • Kim, J.H., Lee, J., Oh, B., et al. 2004. Prediction of phosphorylation sites using SVMs. Bioinformatics 20, 3179-3184.
    • (2004) Bioinformatics , vol.20 , pp. 3179-3184
    • Kim, J.H.1    Lee, J.2    Oh, B.3
  • 56
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt, G.J. 1999. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285, 1887-1897.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 57
    • 36749099341 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions for template-based modeling targets
    • Kopp, J., Bordoli, L., Battey, J.N., et al. 2007. Assessment of CASP7 predictions for template-based modeling targets. Proteins 69, Suppl 8, 38-56.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 38-56
    • Kopp, J.1    Bordoli, L.2    Battey, J.N.3
  • 58
    • 22544448378 scopus 로고    scopus 로고
    • Profile-based string kernels for remote homology detection and motif extraction
    • Kuang, R., Ie, E., Wang, K., et al. 2005. Profile-based string kernels for remote homology detection and motif extraction. J. Bioinform. Comput. Biol. 3, 527-550.
    • (2005) J. Bioinform. Comput. Biol. , vol.3 , pp. 527-550
    • Kuang, R.1    Ie, E.2    Wang, K.3
  • 59
    • 8844263749 scopus 로고    scopus 로고
    • A statistical framework for genomic data fusion
    • Lanckriet, G.R., De Bie, T., Cristianini, N., et al. 2004a. A statistical framework for genomic data fusion. Bioinformatics 20, 2626-2635.
    • (2004) Bioinformatics , vol.20 , pp. 2626-2635
    • Lanckriet, G.R.1    De Bie, T.2    Cristianini, N.3
  • 60
    • 2442674422 scopus 로고    scopus 로고
    • Kernel-based data fusion and its application to protein function prediction in yeast
    • Lanckriet, G.R., Deng, M., Cristianini, N., et al. 2004b. Kernel-based data fusion and its application to protein function prediction in yeast. Pac. Symp. Biocomput. 300-311.
    • (2004) Pac. Symp. Biocomput. , pp. 300-311
    • Lanckriet, G.R.1    Deng, M.2    Cristianini, N.3
  • 61
    • 38349144394 scopus 로고    scopus 로고
    • Understanding the molecular machinery of genetics through 3D structures
    • Laskowski, R.A., and Thornton, J.M. 2008. Understanding the molecular machinery of genetics through 3D structures. Nat. Rev. Genet. 9, 141-151.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 141-151
    • Laskowski, R.A.1    Thornton, J.M.2
  • 62
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: A server for predicting protein function from 3D structure
    • Laskowski, R.A., Watson, J.D., and Thornton, J.M. 2005a. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res. 33, W89-W93.
    • (2005) Nucleic Acids Res. , vol.33
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 63
    • 22544486576 scopus 로고    scopus 로고
    • Protein function prediction using local 3D templates
    • Laskowski, R.A., Watson, J.D., and Thornton, J.M. 2005b. Protein function prediction using local 3D templates. J. Mol. Biol. 351, 614-626.
    • (2005) J. Mol. Biol. , vol.351 , pp. 614-626
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 64
    • 39649088661 scopus 로고    scopus 로고
    • Conformational switching upon phosphorylation: A predictive framework based on energy landscape principles
    • Latzer, J., Shen, T., and Wolynes, P.G. 2008. Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry, 47, 2110-2122.
    • (2008) Biochemistry , vol.47 , pp. 2110-2122
    • Latzer, J.1    Shen, T.2    Wolynes, P.G.3
  • 65
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee, D., Redfern, O., and Orengo, C. 2007. Predicting protein function from sequence and structure. Nat. Rev. Mol. Cell Biol. 8, 995-1005.
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 66
    • 33644876212 scopus 로고    scopus 로고
    • DbPTM: An information repository of protein post-translational modification
    • Lee, T.Y., Huang, H.D., Hung, J.H., et al. 2006. dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 34, D622-D627.
    • (2006) Nucleic Acids Res. , vol.34
    • Lee, T.Y.1    Huang, H.D.2    Hung, J.H.3
  • 67
    • 0036358995 scopus 로고    scopus 로고
    • The spectrum kernel: A string kernel for SVM protein classification
    • Leslie, C., Eskin, E., and Noble, W.S. 2002. The spectrum kernel: a string kernel for SVM protein classification. Pac. Symp. Biocomput. 564-575.
    • (2002) Pac. Symp. Biocomput. , pp. 564-575
    • Leslie, C.1    Eskin, E.2    Noble, W.S.3
  • 68
    • 84883575579 scopus 로고    scopus 로고
    • Fast string kernels using inexact matching for protein sequences
    • Leslie, C., and Kuang, R. 2004. Fast string kernels using inexact matching for protein sequences. J. Mach. Learn. Res. 5, 1435-1455.
    • (2004) J. Mach. Learn. Res. , vol.5 , pp. 1435-1455
    • Leslie, C.1    Kuang, R.2
  • 69
    • 0042622410 scopus 로고    scopus 로고
    • WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures
    • Liang, M.P., Banatao, D.R., Klein, T.E., et al. 2003. WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures, Nucleic Acids Res. 31, 3324-3327.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3324-3327
    • Liang, M.P.1    Banatao, D.R.2    Klein, T.E.3
  • 71
    • 17244367767 scopus 로고    scopus 로고
    • Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis
    • Mooney, S.D. 2005. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief. Bioinform. 6, 44-56.
    • (2005) Brief. Bioinform. , vol.6 , pp. 44-56
    • Mooney, S.D.1
  • 72
    • 28644444803 scopus 로고    scopus 로고
    • Structural characterization of proteins using residue environments
    • Mooney, S.D., Liang, M.H., DeConde, R., et al. 2005. Structural characterization of proteins using residue environments. Proteins 61, 741-747.
    • (2005) Proteins , vol.61 , pp. 741-747
    • Mooney, S.D.1    Liang, M.H.2    Deconde, R.3
  • 73
    • 0025719208 scopus 로고
    • Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
    • Nussinov, R., and Wolfson, H.J. 1991. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. U.S.A. 88, 10495-10499.
    • (1991) Proc. Natl. Acad. Sci. U.S.A. , vol.88 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.J.2
  • 74
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer, J.C., Cantley, L.C., and Yaffe, M.B. 2003. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31, 3635-3641.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 75
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • Ondrechen, M.J., Clifton, J.G., and Ringe, D. 2001. THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. U.S.A. 98, 12473-12478.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 12473-12478
    • Ondrechen, M.J.1    Clifton, J.G.2    Ringe, D.3
  • 76
    • 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 13, 121-130.
    • (2005) Structure , vol.13 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 77
    • 6944227836 scopus 로고    scopus 로고
    • Automated prediction of protein function and detection of functional sites from structure
    • Pazos, F., and Sternberg, M.J. 2004. Automated prediction of protein function and detection of functional sites from structure. Proc. Natl. Acad. Sci. U.S.A. 101, 14754-14759.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 14754-14759
    • Pazos, F.1    Sternberg, M.J.2
  • 78
    • 0003243224 scopus 로고    scopus 로고
    • Probabilistic outputs for support vector machines and comparison to regularized likelihood methods, 61-74
    • Smola, A.J., Bartlett, P., Scholkopf, B. and Schuurmans D., eds. MIT Press, Cambridge, MA
    • Platt, J.C. 1999. Probabilistic outputs for support vector machines and comparison to regularized likelihood methods, 61-74. In Smola, A.J., Bartlett, P., Scholkopf, B. and Schuurmans, D., eds. Advances in Large Margin Classifiers. MIT Press, Cambridge, MA.
    • (1999) Advances in Large Margin Classifiers
    • Platt, J.C.1
  • 79
    • 0036568293 scopus 로고    scopus 로고
    • Prediction of coordination number and relative solvent accessibility in proteins
    • Pollastri, G., Baldi, P., Fariselli, P., et al. 2002. Prediction of coordination number and relative solvent accessibility in proteins. Proteins 47, 142-153.
    • (2002) Proteins , vol.47 , pp. 142-153
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3
  • 80
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter, C.T., Bartlett, G.J. and Thornton, J.M. 2004. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res. 32, D129-D133.
    • (2004) Nucleic Acids Res. , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 81
    • 33846672214 scopus 로고    scopus 로고
    • Biological network comparison using graphlet degree distribution
    • Przulj, N. 2007. Biological network comparison using graphlet degree distribution. Bioinformatics 23, e177-e183.
    • (2007) Bioinformatics , vol.23
    • Przulj, N.1
  • 82
    • 12344273375 scopus 로고    scopus 로고
    • Modeling interactome: Scale-free or geometric?
    • Przulj, N., Corneil, D.G., and Jurisica, I. 2004. Modeling interactome: scale-free or geometric? Bioinformatics 20, 3508-3515.
    • (2004) Bioinformatics , vol.20 , pp. 3508-3515
    • Przulj, N.1    Corneil, D.G.2    Jurisica, I.3
  • 83
    • 0029867420 scopus 로고    scopus 로고
    • Conformational effects of serine phosphorylation in phospholamban peptides
    • Quirk, P.G., Patchell, V.B., Colyer, J., et al. 1996. Conformational effects of serine phosphorylation in phospholamban peptides. Eur. J. Biochem. 236, 85-91.
    • (1996) Eur. J. Biochem. , vol.236 , pp. 85-91
    • Quirk, P.G.1    Patchell, V.B.2    Colyer, J.3
  • 84
    • 23844480138 scopus 로고    scopus 로고
    • Graph kernels for chemical informatics
    • Ralaivola, L., Swamidass, S.J., Saigo, H., et al. 2005. Graph kernels for chemical informatics. Neural Netw. 18, 1093-1110.
    • (2005) Neural Netw. , vol.18 , pp. 1093-1110
    • Ralaivola, L.1    Swamidass, S.J.2    Saigo, H.3
  • 85
    • 44949137643 scopus 로고    scopus 로고
    • Determinants of protein function revealed by combinatorial entropy optimization
    • Reva, B., Antipin, Y., and Sander, C. 2007. Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol. 8, R232.
    • (2007) Genome Biol. , vol.8
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 86
    • 38949156579 scopus 로고    scopus 로고
    • Linear-time computation of similarity measures for sequential data
    • Rieck, K., and Laskov, P. 2008. Linear-time computation of similarity measures for sequential data. J. Mach. Learn. Res. 9, 23-48.
    • (2008) J. Mach. Learn. Res. , vol.9 , pp. 23-48
    • Rieck, K.1    Laskov, P.2
  • 87
    • 0346731042 scopus 로고    scopus 로고
    • Automatic prediction of protein function
    • Rost, B., Liu, J., Nair, R., et al. 2003. Automatic prediction of protein function. Cell Mol. Life Sci. 60, 2637-2650.
    • (2003) Cell Mol. Life Sci. , vol.60 , pp. 2637-2650
    • Rost, B.1    Liu, J.2    Nair, R.3
  • 88
    • 21144458164 scopus 로고    scopus 로고
    • Immunoaffinity profiling of tyrosine phosphorylation in cancer cells
    • Rush, J., Moritz, A., Lee, K.A., et al. 2005. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat. Biotechnol. 23, 94-101.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 94-101
    • Rush, J.1    Moritz, A.2    Lee, K.A.3
  • 89
    • 0032568859 scopus 로고    scopus 로고
    • Detection of protein three-dimensional side-chain patterns: New examples of convergent evolution
    • Russell, R.B. 1998. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J. Mol. Biol. 279, 1211-1227.
    • (1998) J. Mol. Biol. , vol.279 , pp. 1211-1227
    • Russell, R.B.1
  • 90
    • 4444292685 scopus 로고    scopus 로고
    • Scholkopf, B., Tsuda, K., and Vert, J.-P., eds. MIT Press, Cambridge, MA
    • Scholkopf, B., Tsuda, K., and Vert, J.-P., eds. 2004. Kernel Methods in Computational Biology. MIT Press, Cambridge, MA.
    • (2004) Kernel Methods in Computational Biology
  • 91
    • 24644442164 scopus 로고    scopus 로고
    • The folding energy landscape and phosphorylation: Modeling the conformational switch of the NFAT regulatory domain
    • Shen, T., Zong, C., Hamelberg, D., et al. 2005. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. FASEB J. 19, 1389-1395.
    • (2005) FASEB J. , vol.19 , pp. 1389-1395
    • Shen, T.1    Zong, C.2    Hamelberg, D.3
  • 92
    • 34447502162 scopus 로고    scopus 로고
    • Prediction and assignment of function for a divergent N-succinyl amino acid racemase
    • Song, L., Kalyanaraman, C., Fedorov, A.A., et al. 2007. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat. Chem. Biol. 3, 486-491.
    • (2007) Nat. Chem. Biol. , vol.3 , pp. 486-491
    • Song, L.1    Kalyanaraman, C.2    Fedorov, A.A.3
  • 93
    • 0035830403 scopus 로고    scopus 로고
    • Influence of myristoylation, phosphorylation, and deamidation on the structural behavior of the N-terminus of the catalytic subunit of cAMP-dependent protein kinase
    • Tholey, A., Pipkorn, R., Bossemeyer, D., et al. 2001. Influence of myristoylation, phosphorylation, and deamidation on the structural behavior of the N-terminus of the catalytic subunit of cAMP-dependent protein kinase. Biochemistry 40, 225-231.
    • (2001) Biochemistry , vol.40 , pp. 225-231
    • Tholey, A.1    Pipkorn, R.2    Bossemeyer, D.3
  • 94
    • 0030724039 scopus 로고    scopus 로고
    • TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
    • Wallace, A.C., Borkakoti, N., and Thornton, J.M. 1997. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6, 2308-2323.
    • (1997) Protein Sci. , vol.6 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 95
    • 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., and Thornton, J.M. 1996. 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) Protein Sci. , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 96
    • 0037459071 scopus 로고    scopus 로고
    • Functional sites in protein families uncovered via an objective and automated graph theoretic approach
    • Wangikar, P.P., Tendulkar, A.V., Ramya, S., et al. 2003. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J. Mol. Biol. 326, 955-978.
    • (2003) J. Mol. Biol. , vol.326 , pp. 955-978
    • Wangikar, P.P.1    Tendulkar, A.V.2    Ramya, S.3
  • 97
  • 98
    • 0031626949 scopus 로고    scopus 로고
    • Recognizing protein binding sites using statistical descriptions of their 3D environments
    • Wei, L., and Altman, R.B. 1998. Recognizing protein binding sites using statistical descriptions of their 3D environments. Pac. Symp. Biocomput. 497-508.
    • (1998) Pac. Symp. Biocomput. , pp. 497-508
    • Wei, L.1    Altman, R.B.2
  • 99
    • 4444296254 scopus 로고    scopus 로고
    • Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function
    • Wei, L., and Altman, R.B. 2003. Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function. J. Bioinform. Comput. Biol. 1, 119-138.
    • (2003) J. Bioinform. Comput. Biol. , vol.1 , pp. 119-138
    • Wei, L.1    Altman, R.B.2
  • 101
    • 0024046461 scopus 로고
    • Analysis and prediction of the location of catalytic residues in enzymes
    • Zvelebil, M.J., and Sternberg, M.J. 1988. Analysis and prediction of the location of catalytic residues in enzymes. Protein Eng. 2, 127-138.
    • (1988) Protein Eng. , vol.2 , pp. 127-138
    • Zvelebil, M.J.1    Sternberg, M.J.2


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