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Volumn 26, Issue 14, 2010, Pages 1714-1722

Prediction of protease substrates using sequence and structure features

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METAZOA;

EID: 77954481626     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq267     Document Type: Article
Times cited : (57)

References (49)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M. et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 2
    • 23144444029 scopus 로고    scopus 로고
    • GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
    • Backes, C. et al. (2005) GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res., 33, W208-W213.
    • (2005) Nucleic Acids Res. , vol.33
    • Backes, C.1
  • 3
    • 22544474376 scopus 로고    scopus 로고
    • PoPS: a computational tool for modeling and predicting protease specificity
    • Boyd, S.E. et al. (2005) PoPS: a computational tool for modeling and predicting protease specificity. J. Bioinform. Comput. Biol., 3, 551-585.
    • (2005) J. Bioinform. Comput. Biol. , vol.3 , pp. 551-585
    • Boyd, S.E.1
  • 4
    • 23844457176 scopus 로고    scopus 로고
    • Use of protease proteomics to discover granzyme B substrates
    • Bredemeyer, A.J. et al. (2005) Use of protease proteomics to discover granzyme B substrates. Immunol. Res., 32, 143-153.
    • (2005) Immunol. Res. , vol.32 , pp. 143-153
    • Bredemeyer, A.J.1
  • 5
    • 33645034411 scopus 로고    scopus 로고
    • Structural prediction of peptides binding to MHC class I molecules
    • Bui, H.H. et al. (2006) Structural prediction of peptides binding to MHC class I molecules. Proteins, 63, 43-52.
    • (2006) Proteins , vol.63 , pp. 43-52
    • Bui, H.H.1
  • 6
    • 0033588955 scopus 로고    scopus 로고
    • Cleavage by granzyme B is strongly predictive of autoantigen status: implications for initiation of autoimmunity
    • Casciola-Rosen, L. et al. (1999) Cleavage by granzyme B is strongly predictive of autoantigen status: implications for initiation of autoimmunity. J. Exp. Med., 190, 815-826.
    • (1999) J. Exp. Med. , vol.190 , pp. 815-826
    • Casciola-Rosen, L.1
  • 7
    • 4143110083 scopus 로고    scopus 로고
    • Systematic analysis of added-value in simple comparative models of protein structure
    • Chakravarty, S. and Sanchez, R. (2004) Systematic analysis of added-value in simple comparative models of protein structure. Structure, 12, 1461-1470.
    • (2004) Structure , vol.12 , pp. 1461-1470
    • Chakravarty, S.1    Sanchez, R.2
  • 8
    • 51349085386 scopus 로고    scopus 로고
    • Predicting PDZ domain-peptide interactions from primary sequences
    • Chen, J.R. et al. (2008) Predicting PDZ domain-peptide interactions from primary sequences. Nat. Biotechnol., 26, 1041-1045.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1041-1045
    • Chen, J.R.1
  • 9
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: a sequence logo generator
    • Crooks, G.E. et al. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
    • (2004) Genome Res. , vol.14 , pp. 1188-1190
    • Crooks, G.E.1
  • 10
    • 49549113643 scopus 로고    scopus 로고
    • Global mapping of the topography and magnitude of proteolytic events in apoptosis
    • Dix, M.M. et al. (2008) Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell, 134, 679-691.
    • (2008) Cell , vol.134 , pp. 679-691
    • Dix, M.M.1
  • 11
    • 55549141879 scopus 로고    scopus 로고
    • How well can the accuracy of comparative protein structure models be predicted
    • Eramian, D. et al. (2008) How well can the accuracy of comparative protein structure models be predicted? Protein Sci., 17, 1881-1893.
    • (2008) Protein Sci. , vol.17 , pp. 1881-1893
    • Eramian, D.1
  • 12
    • 33947315301 scopus 로고    scopus 로고
    • A neural strategy for the inference of SH3 domain-peptide interaction specificity
    • Ferraro, E. et al. (2005) A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinformatics, 6 (Suppl. 4), S13.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 4
    • Ferraro, E.1
  • 13
    • 29144473665 scopus 로고    scopus 로고
    • CaSPredictor: a new computer-based tool for caspase substrate prediction
    • Garay-Malpartida, H.M. et al. (2005) CaSPredictor: a new computer-based tool for caspase substrate prediction. Bioinformatics, 21 (Suppl. 1), i169-i176.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Garay-Malpartida, H.M.1
  • 14
    • 66149146342 scopus 로고    scopus 로고
    • Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains
    • Hou, T. et al. (2009) Characterization of domain-peptide interaction interface: a generic structure-based model to decipher the binding specificity of SH3 domains. Mol. Cell Proteomics, 8, 639-649.
    • (2009) Mol. Cell Proteomics , vol.8 , pp. 639-649
    • Hou, T.1
  • 15
    • 0032539578 scopus 로고    scopus 로고
    • The structural aspects of limited proteolysis of native proteins
    • Hubbard, S.J. (1998) The structural aspects of limited proteolysis of native proteins. Biochim. Biophys. Acta, 1382, 191-206.
    • (1998) Biochim. Biophys. Acta , vol.1382 , pp. 191-206
    • Hubbard, S.J.1
  • 16
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    • Jacob, L. and Vert, J.P. (2008) Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics, 24, 358-366.
    • (2008) Bioinformatics , vol.24 , pp. 358-366
    • Jacob, L.1    Vert, J.P.2
  • 17
    • 34547643210 scopus 로고    scopus 로고
    • PDZ domains: folding and binding
    • Jemth, P. and Gianni, S. (2007) PDZ domains: folding and binding. Biochemistry, 46, 8701-8708.
    • (2007) Biochemistry , vol.46 , pp. 8701-8708
    • Jemth, P.1    Gianni, S.2
  • 18
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale SVM learning practical
    • Scholkopf, B. et al. (eds) MIT-Press, Boston
    • Joachims, T. (1999) Making large-scale SVM learning practical. In Scholkopf, B. et al. (eds) Advances in Kernel Methods - Support Vector Learning. MIT-Press, Boston, pp. 169--184.
    • (1999) Advances in Kernel Methods - Support Vector Learning , pp. 169-184
    • Joachims, T.1
  • 19
    • 50249184065 scopus 로고    scopus 로고
    • Caspase cleavage is not for everyone
    • Johnson, C.E. and Kornbluth, S. (2008) Caspase cleavage is not for everyone. Cell, 134, 720-721.
    • (2008) Cell , vol.134 , pp. 720-721
    • Johnson, C.E.1    Kornbluth, S.2
  • 20
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 21
    • 0242362157 scopus 로고    scopus 로고
    • Prediction of disordered regions in proteins from position specific score matrices
    • Jones, D.T. and Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins, 53 (Suppl. 6), 573-578.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 573-578
    • Jones, D.T.1    Ward, J.J.2
  • 22
    • 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
  • 23
    • 42649119825 scopus 로고    scopus 로고
    • The SH3 domain-a family of versatile peptide- and protein- recognition module
    • Kaneko, T. et al. (2008) The SH3 domain-a family of versatile peptide- and protein- recognition module. Front. Biosci., 13, 4938-4952.
    • (2008) Front. Biosci. , vol.13 , pp. 4938-4952
    • Kaneko, T.1
  • 24
    • 0034700180 scopus 로고    scopus 로고
    • Survival motor neuron protein modulates neuron-specific apoptosis
    • Kerr, D.A. et al. (2000) Survival motor neuron protein modulates neuron-specific apoptosis. Proc. Natl Acad. Sci. USA, 97, 13312-13317.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 13312-13317
    • Kerr, D.A.1
  • 25
    • 33748779522 scopus 로고    scopus 로고
    • Granzyme B proteolyzes receptors important to proliferation and survival, tipping the balance toward apoptosis
    • Loeb, C.R.K. et al. (2006) Granzyme B proteolyzes receptors important to proliferation and survival, tipping the balance toward apoptosis. J. Biol. Chem., 281, 28326-28335.
    • (2006) J. Biol. Chem. , vol.281 , pp. 28326-28335
    • Loeb, C.R.K.1
  • 26
    • 0038824700 scopus 로고    scopus 로고
    • Toward computer-based cleavage site prediction of cysteine endopeptidases
    • Lohmüller, T. et al. (2003) Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol. Chem., 384, 899-909.
    • (2003) Biol. Chem. , vol.384 , pp. 899-909
    • Lohmüller, T.1
  • 27
    • 33947426526 scopus 로고    scopus 로고
    • The CASBAH: a searchable database of caspase substrates
    • Lüthi, A.U. and Martin, S.J. (2007) The CASBAH: a searchable database of caspase substrates. Cell Death Differ., 14, 641-650.
    • (2007) Cell Death Differ. , vol.14 , pp. 641-650
    • Lüthi, A.U.1    Martin, S.J.2
  • 28
    • 52649141086 scopus 로고    scopus 로고
    • Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
    • Mahrus, S. et al. (2008) Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell, 134, 866-876.
    • (2008) Cell , vol.134 , pp. 866-876
    • Mahrus, S.1
  • 29
    • 0036602982 scopus 로고    scopus 로고
    • Cytotoxic T lymphocytes in autoimmune and degenerative CNS diseases
    • Neumann, H. et al. (2002) Cytotoxic T lymphocytes in autoimmune and degenerative CNS diseases. Trends Neurosci., 25, 313-319.
    • (2002) Trends Neurosci. , vol.25 , pp. 313-319
    • Neumann, H.1
  • 30
    • 0037428232 scopus 로고    scopus 로고
    • Apoptosis. Life and death decisions
    • Nicholson, D.W. and Thornberry, N.A. (2003) Apoptosis. Life and death decisions. Science, 299, 214-215.
    • (2003) Science , vol.299 , pp. 214-215
    • Nicholson, D.W.1    Thornberry, N.A.2
  • 31
    • 64549090599 scopus 로고    scopus 로고
    • The biology of cytotoxic cell granule exocytosis pathway: granzymes have evolved to induce cell death and inflammation
    • Pardo, J. et al. (2009) The biology of cytotoxic cell granule exocytosis pathway: granzymes have evolved to induce cell death and inflammation. Microbes Infect., 11, 452-459.
    • (2009) Microbes Infect. , vol.11 , pp. 452-459
    • Pardo, J.1
  • 32
    • 58149187896 scopus 로고    scopus 로고
    • MODBASE, a database of annotated comparative protein structure models and associated resources
    • Pieper, U. et al. (2009) MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res., 37, D347-354.
    • (2009) Nucleic Acids Res. , vol.37
    • Pieper, U.1
  • 33
    • 17944366977 scopus 로고    scopus 로고
    • Heat-shock protein 70 antagonizes apoptosis-inducing factor
    • Ravagnan, L. et al. (2001) Heat-shock protein 70 antagonizes apoptosis-inducing factor. Nat. Cell Biol., 3, 839-843.
    • (2001) Nat. Cell Biol. , vol.3 , pp. 839-843
    • Ravagnan, L.1
  • 34
    • 0036217977 scopus 로고    scopus 로고
    • Lymphocyte-mediated cytotoxicity
    • Russell, J.H. and Ley, T.J. (2002) Lymphocyte-mediated cytotoxicity. Annu. Rev. Immunol., 20, 323-370.
    • (2002) Annu. Rev. Immunol. , vol.20 , pp. 323-370
    • Russell, J.H.1    Ley, T.J.2
  • 35
    • 0014405092 scopus 로고
    • On the active site of proteases 3. Mapping the active site of papain; specific peptide inhibitors of papain
    • Schechter, I. and Berger, A. (1968) On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain. Biochem. Biophys. Res. Commun., 32, 898-902.
    • (1968) Biochem. Biophys. Res. Commun. , vol.32 , pp. 898-902
    • Schechter, I.1    Berger, A.2
  • 36
    • 69449097120 scopus 로고    scopus 로고
    • Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules
    • Sieker, F. et al. (2009) Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules. Curr. Protein Pept. Sci., 10, 286-296.
    • (2009) Curr. Protein Pept. Sci. , vol.10 , pp. 286-296
    • Sieker, F.1
  • 37
    • 0032847318 scopus 로고    scopus 로고
    • Caspases: preparation and characterization
    • Stennicke, H.R. and Salvesen, G.S. (1999) Caspases: preparation and characterization. Methods, 17, 313-319.
    • (1999) Methods , vol.17 , pp. 313-319
    • Stennicke, H.R.1    Salvesen, G.S.2
  • 38
    • 34547127612 scopus 로고    scopus 로고
    • PDZ domain binding selectivity is optimized across the mouse proteome
    • Stiffler, M.A. et al. (2007) PDZ domain binding selectivity is optimized across the mouse proteome. Science, 317, 364-369.
    • (2007) Science , vol.317 , pp. 364-369
    • Stiffler, M.A.1
  • 39
    • 0030849093 scopus 로고    scopus 로고
    • Acombinatorial approach defines specificities of members of the caspase family and granzyme B Functional relationships established for key mediators of apoptosis
    • Thornberry, N.A. et al. (1997)Acombinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis. J. Biol. Chem., 272, 17907-17911.
    • (1997) J. Biol. Chem. , vol.272 , pp. 17907-17911
    • Thornberry, N.A.1
  • 40
    • 70349832234 scopus 로고    scopus 로고
    • Structural and kinetic determinants of protease substrates
    • Timmer, J. et al. (2009) Structural and kinetic determinants of protease substrates. Nat. Struct. Mol. Biol., 16, 1101-1108.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 1101-1108
    • Timmer, J.1
  • 41
    • 61649102448 scopus 로고    scopus 로고
    • Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs
    • Van Damme, P. et al. (2008) Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs. Mol. Cell Proteomics, 8, 258-272.
    • (2008) Mol. Cell Proteomics , vol.8 , pp. 258-272
    • Van Damme, P.1
  • 42
    • 67649961479 scopus 로고    scopus 로고
    • SitePredicting the cleavage of proteinase substrates
    • Verspurten, J. et al. (2009) SitePredicting the cleavage of proteinase substrates. Trends Biochem. Sci., 34, 319-323.
    • (2009) Trends Biochem. Sci. , vol.34 , pp. 319-323
    • Verspurten, J.1
  • 43
    • 0037109143 scopus 로고    scopus 로고
    • Involvement of survival motor neuron (SMN) protein in cell death
    • Vyas, S. et al. (2002) Involvement of survival motor neuron (SMN) protein in cell death. Hum. Mol. Genet., 11, 2751-2764.
    • (2002) Hum. Mol. Genet. , vol.11 , pp. 2751-2764
    • Vyas, S.1
  • 44
    • 84871967410 scopus 로고    scopus 로고
    • SVM-based prediction of caspase substrate cleavage sites
    • Wee, L.J. et al. (2006) SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics, 7 (Suppl. 5), S14.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 5
    • Wee, L.J.1
  • 45
    • 0032619552 scopus 로고    scopus 로고
    • Proteini dentification and analysis tools in theE xPASy server
    • Wilkins, M.R. et al. (1999) Proteini dentification and analysis tools in theE xPASy server. Methods Mol. Biol., 112, 531-552.
    • (1999) Methods Mol. Biol. , vol.112 , pp. 531-552
    • Wilkins, M.R.1
  • 46
    • 18744369642 scopus 로고    scopus 로고
    • Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks
    • Yang, Z.R. (2005) Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. Bioinformatics, 21, 1831-1837.
    • (2005) Bioinformatics , vol.21 , pp. 1831-1837
    • Yang, Z.R.1
  • 47
    • 77954482190 scopus 로고    scopus 로고
    • Leukocyte recruitment and ischemic brain injury
    • Yilmaz, G. and Granger, D.N. (2010) Leukocyte recruitment and ischemic brain injury. Neuromolecular Med., 12, 193-204.
    • (2010) Neuromolecular Med. , vol.12 , pp. 193-204
    • Yilmaz, G.1    Granger, D.N.2
  • 48
    • 27344458981 scopus 로고    scopus 로고
    • Cysteine protease inhibition prevents mitochondrial apoptosis-inducing factor (AIF) release
    • Yuste, V.J. et al. (2005) Cysteine protease inhibition prevents mitochondrial apoptosis-inducing factor (AIF) release. Cell Death Differ., 12, 1445-1448.
    • (2005) Cell Death Differ. , vol.12 , pp. 1445-1448
    • Yuste, V.J.1
  • 49
    • 33746285302 scopus 로고    scopus 로고
    • An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands
    • Zhang, L. et al. (2006)An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands. Mol. Cell Proteomics, 5, 1224-1232.
    • (2006) Mol. Cell Proteomics , vol.5 , pp. 1224-1232
    • Zhang, L.1


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