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Volumn 30, Issue 12, 2014, Pages 1681-1689

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

EID: 84907550746     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu106     Document Type: Article
Times cited : (7)

References (37)
  • 1
    • 79955389305 scopus 로고    scopus 로고
    • Data-driven high-throughput prediction of the 3-D structure of small molecules: Review and progress
    • Andronico, A. et al. (2011) Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. J. Chem. Inf. Model., 51, 760-766.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 760-766
    • Andronico, A.1
  • 2
    • 0033957834 scopus 로고    scopus 로고
    • The swiss-prot protein sequence database and its supplement trembl in 2000
    • Bairoch, A. and Apweiler, R. (2000) The swiss-prot protein sequence database and its supplement trembl in 2000. Nucleic Acids Res., 28, 45-48.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 4
    • 84874737574 scopus 로고    scopus 로고
    • A protein-dependent side-chain rotamer library
    • Bhuyan, M.S. and Gao, X. (2011 A protein-dependent side-chain rotamer library. BMC Bioinformatics, 12 (Suppl. 14), S10.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 14
    • Bhuyan, M.S.1    Gao, X.2
  • 5
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • Blom, N. et al. (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
  • 6
    • 2942564430 scopus 로고    scopus 로고
    • Prediction of post-translational glycosylation and phosphor-ylation of proteins from the amino acid sequence
    • Blom, N. et al. (2004) Prediction of post-translational glycosylation and phosphor-ylation of proteins from the amino acid sequence. Proteomics, 4, 1633-1649.
    • (2004) Proteomics , vol.4 , pp. 1633-1649
    • Blom, N.1
  • 7
    • 78651320816 scopus 로고    scopus 로고
    • Phospho.ELM: A database of phosphorylation sitesupdate 2011
    • Dinkel, H. et al. (2010) Phospho.ELM: a database of phosphorylation sitesupdate 2011. Nucleic Acids Res., 39, D261-D267.
    • (2010) Nucleic Acids Res. , vol.39
    • Dinkel, H.1
  • 8
    • 84861818648 scopus 로고    scopus 로고
    • Expanding molecular modeling and design tools to non-natural sidechains
    • Gfeller, D. et al. (2012) Expanding molecular modeling and design tools to non-natural sidechains. J. Comput. Chem., 33, 1525-1535.
    • (2012) J. Comput. Chem. , vol.33 , pp. 1525-1535
    • Gfeller, D.1
  • 9
    • 78651277460 scopus 로고    scopus 로고
    • Phosida 2011: The posttranslational modification database
    • Gnad, F. et al. (2011 Phosida 2011: the posttranslational modification database. Nucleic Acids Res., 39 (Suppl. 1, D253-D260.
    • (2011) Nucleic Acids Res. , vol.39 , Issue.SUPPL. 1
    • Gnad, F.1
  • 10
    • 62149135362 scopus 로고    scopus 로고
    • Prediction of glycosylation sites using random forests
    • Hamby, S. and Hirst, J. (2008 Prediction of glycosylation sites using random forests. BMC Bioinformatics, 9, 500.
    • (2008) BMC Bioinformatics , vol.9 , pp. 500
    • Hamby, S.1    Hirst, J.2
  • 11
    • 34250792960 scopus 로고    scopus 로고
    • Irecs: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models
    • Hartmann, C. et al. (2007) Irecs: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci., 16, 1294-1307.
    • (2007) Protein Sci. , vol.16 , pp. 1294-1307
    • Hartmann, C.1
  • 12
    • 84857047339 scopus 로고    scopus 로고
    • Phosphositeplus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Hornbeck, P.V. et al. (2012) Phosphositeplus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res., 40, D261-D270.
    • (2012) Nucleic Acids Res. , vol.40
    • Hornbeck, P.V.1
  • 13
    • 13644257223 scopus 로고    scopus 로고
    • Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
    • Julenius, K. et al. (2005) Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology, 15, 153-164.
    • (2005) Glycobiology , vol.15 , pp. 153-164
    • Julenius, K.1
  • 14
    • 58149193222 scopus 로고    scopus 로고
    • Human protein reference database2009 update
    • Keshava Prasad, T.S. et al. (2009) Human protein reference database2009 update. Nucleic Acids Res., 37 (Suppl. 1), D767-D772.
    • (2009) Nucleic Acids Res. , vol.37 , Issue.SUPPL. 1
    • Keshava Prasad, T.S.1
  • 15
    • 84910679144 scopus 로고    scopus 로고
    • Proteome-wide post-translation al modification statistics: Frequency analysis and curation of the swiss-prot database
    • Khoury, G.A. et al. (2011) Proteome-wide post-translation al modification statistics: frequency analysis and curation of the swiss-prot database. Sci. Rep., 1, 90.
    • (2011) Sci. Rep. , vol.1 , pp. 90
    • Khoury, G.A.1
  • 16
    • 8844219516 scopus 로고    scopus 로고
    • Prediction of phosphorylation sites using SVMs
    • Kim, J.H. et al. (2004) Prediction of phosphorylation sites using SVMs. Bioinformatics, 20, 3179-3184.
    • (2004) Bioinformatics , vol.20 , pp. 3179-3184
    • Kim, J.H.1
  • 17
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • Krivov, G.G. et al. (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77, 778-795.
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1
  • 18
    • 78650905964 scopus 로고    scopus 로고
    • ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
    • Leaver-Fay, A. et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol., 487, 545-574.
    • (2011) Methods Enzymol. , vol.487 , pp. 545-574
    • Leaver-Fay, A.1
  • 19
    • 33646887253 scopus 로고    scopus 로고
    • Predicting O-glycosylation sites in mammalian proteins by using SVMs
    • Li, S. et al. (2006) Predicting O-glycosylation sites in mammalian proteins by using SVMs. Comput. Biol. Chem., 30, 203-208.
    • (2006) Comput. Biol. Chem. , vol.30 , pp. 203-208
    • Li, S.1
  • 20
    • 68949108329 scopus 로고    scopus 로고
    • Improved prediction of lysine acetylation by support vector machines
    • Li, S. et al. (2009) Improved prediction of lysine acetylation by support vector machines. Protein Pept. Lett., 16, 977-983.
    • (2009) Protein Pept. Lett. , vol.16 , pp. 977-983
    • Li, S.1
  • 21
    • 80053986637 scopus 로고    scopus 로고
    • Fast and accurate prediction of protein side-chain conformations
    • Liang, S. et al. (2011) Fast and accurate prediction of protein side-chain conformations. Bioinformatics, 27, 2913-2914.
    • (2011) Bioinformatics , vol.27 , pp. 2913-2914
    • Liang, S.1
  • 22
    • 0034663722 scopus 로고    scopus 로고
    • The penultimate rotamer library
    • Lovell, S.C. et al. (2000) The penultimate rotamer library. Proteins, 40, 389-408.
    • (2000) Proteins , vol.40 , pp. 389-408
    • Lovell, S.C.1
  • 23
    • 50049116635 scopus 로고    scopus 로고
    • OPUS-Rota: A fast and accurate method for side-chain modeling
    • Lu, M. et al. (2008) OPUS-Rota: a fast and accurate method for side-chain modeling. Protein Sci., 17, 1576-1585.
    • (2008) Protein Sci. , vol.17 , pp. 1576-1585
    • Lu, M.1
  • 24
    • 83555178443 scopus 로고    scopus 로고
    • Sidepro: A novel machine learning approach for the fast and accurate prediction of side-chain conformations
    • Nagata, K. et al. (2012) Sidepro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins, 80, 142-153.
    • (2012) Proteins , vol.80 , pp. 142-153
    • Nagata, K.1
  • 25
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
    • Obenauer, J.C. et al. (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
  • 26
    • 80053512597 scopus 로고    scopus 로고
    • Open babel: An open chemical toolbox
    • O'Boyle, N. et al. (2011) Open babel: an open chemical toolbox. J. Chemoinform., 3, 33.
    • (2011) J. Chemoinform. , vol.3 , pp. 33
    • O'Boyle, N.1
  • 27
    • 84864743678 scopus 로고    scopus 로고
    • AMS 4.0: Consensus prediction of post-translational modifications in protein sequences
    • Plewczynski, D. et al. (2012) AMS 4.0: consensus prediction of post-translational modifications in protein sequences. Amino Acids, 43, 573-582.
    • (2012) Amino Acids , vol.43 , pp. 573-582
    • Plewczynski, D.1
  • 28
    • 67650720512 scopus 로고    scopus 로고
    • Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0
    • Ren, J. et al. (2009) Systematic study of protein sumoylation: development of a site-specific predictor of SUMOsp 2.0. Proteomics, 9, 3409-3412.
    • (2009) Proteomics , vol.9 , pp. 3409-3412
    • Ren, J.1
  • 29
    • 84858266350 scopus 로고    scopus 로고
    • Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design
    • Renfrew, P.D. et al. (2012) Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. PLoS One, 7, e32637.
    • (2012) PLoS One , vol.7
    • Renfrew, P.D.1
  • 30
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali, A. and Blundell, T. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 31
    • 79251565520 scopus 로고    scopus 로고
    • The Dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water
    • Scouras, AD. and Daggett, V. (2011) The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Protein Sci., 20, 341-352.
    • (2011) Protein Sci. , vol.20 , pp. 341-352
    • Scouras, A.D.1    Daggett, V.2
  • 32
    • 79958079887 scopus 로고    scopus 로고
    • A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
    • Shapovalov, M.V. and Dunbrack, R.L. Jr. (2011) A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure, 19, 844-858.
    • (2011) Structure , vol.19 , pp. 844-858
    • Shapovalov, M.V.1    Dunbrack, Jr.R.L.2
  • 33
    • 40249113353 scopus 로고    scopus 로고
    • Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection
    • Wan, J. et al. (2008) M eta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection. Nucleic Acids Res., 36, e22.
    • (2008) Nucleic Acids Res. , vol.36
    • Wan, J.1
  • 34
    • 62649104324 scopus 로고    scopus 로고
    • Expanding the genetic code for biological studies
    • Wang, Q. et al. (2009) Expanding the genetic code for biological studies. Chem. Biol., 16, 323.
    • (2009) Chem. Biol. , vol.16 , pp. 323
    • Wang, Q.1
  • 35
    • 27744485401 scopus 로고    scopus 로고
    • Adding amino acids to the genetic repertoire
    • Xie, J. and Schultz, P.G. (2005) Adding amino acids to the genetic repertoire. Curr. Opin. Chem. Biol., 9, 548-554.
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 548-554
    • Xie, J.1    Schultz, P.G.2
  • 36
    • 39449086135 scopus 로고    scopus 로고
    • A novel method for high accuracy sumoylation from protein sequences
    • Xu, J. et al. (2008) A novel method for high accuracy sumoylation from protein sequences. BMC Bioinformatics, 9, 8.
    • (2008) BMC Bioinformatics , vol.9 , pp. 8
    • Xu, J.1
  • 37
    • 80755168412 scopus 로고    scopus 로고
    • Rasp: Rapid modeling of protein side-chain conformations
    • Zhichao, M. et al. (2011) Rasp: rapid modeling of protein side-chain conformations. Bioinformatics, 27, 3117-3122.
    • (2011) Bioinformatics , vol.27 , pp. 3117-3122
    • Zhichao, M.1


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