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Volumn 14, Issue SUPPL7, 2013, Pages

Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CENTRALIZED RESOURCES; DESCRIPTIVE STATISTICS; INFORMATION SOURCES; INTRINSIC DISORDER; INTRINSICALLY DISORDERED PROTEINS; MODEL ORGANISMS; WEIGHTING SCHEME;

EID: 84887176187     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S7-S3     Document Type: Article
Times cited : (27)

References (36)
  • 2
    • 79958044914 scopus 로고    scopus 로고
    • Unstructural biology coming of age
    • 10.1016/j.sbi.2011.03.012, 21514142
    • Tompa P. Unstructural biology coming of age. Curr Opin Struct Biol 2011, 21:419-425. 10.1016/j.sbi.2011.03.012, 21514142.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 419-425
    • Tompa, P.1
  • 4
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
    • 10.1006/jmbi.1999.3110, 10550212
    • Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 1999, 293:321-331. 10.1006/jmbi.1999.3110, 10550212.
    • (1999) J Mol Biol , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 5
    • 0034867975 scopus 로고    scopus 로고
    • The protein trinity--linking function and disorder
    • 10.1038/nbt0901-805, 11533628
    • Dunker AK, Obradovic Z. The protein trinity--linking function and disorder. Nat Biotechnol 2001, 19:805-806. 10.1038/nbt0901-805, 11533628.
    • (2001) Nat Biotechnol , vol.19 , pp. 805-806
    • Dunker, A.K.1    Obradovic, Z.2
  • 6
    • 0036803243 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins
    • 10.1016/S0968-0004(02)02169-2, 12368089
    • Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci 2002, 27:527-533. 10.1016/S0968-0004(02)02169-2, 12368089.
    • (2002) Trends Biochem. Sci , vol.27 , pp. 527-533
    • Tompa, P.1
  • 7
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • 10.1016/j.jmb.2004.02.002, 15019783
    • Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004, 337:635-645. 10.1016/j.jmb.2004.02.002, 15019783.
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 8
    • 84859361768 scopus 로고    scopus 로고
    • Structural disorder in eukaryotes
    • 10.1371/journal.pone.0034687, 3320622, 22496841
    • Pancsa R, Tompa P. Structural disorder in eukaryotes. PLoS ONE 2012, 7:e34687. 10.1371/journal.pone.0034687, 3320622, 22496841.
    • (2012) PLoS ONE , vol.7
    • Pancsa, R.1    Tompa, P.2
  • 9
    • 37749053887 scopus 로고    scopus 로고
    • Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions
    • 10.1016/j.tibs.2007.10.003, 18054235
    • Tompa P, Fuxreiter M. Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci 2008, 33:2-8. 10.1016/j.tibs.2007.10.003, 18054235.
    • (2008) Trends Biochem Sci , vol.33 , pp. 2-8
    • Tompa, P.1    Fuxreiter, M.2
  • 10
    • 63549102895 scopus 로고    scopus 로고
    • Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis
    • 10.1371/journal.pcbi.1000316, 2646137, 19282967
    • Fong JH, Shoemaker BA, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV, Panchenko AR. Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. PLoS Comput Biol 2009, 5:e1000316. 10.1371/journal.pcbi.1000316, 2646137, 19282967.
    • (2009) PLoS Comput Biol , vol.5
    • Fong, J.H.1    Shoemaker, B.A.2    Garbuzynskiy, S.O.3    Lobanov, M.Y.4    Galzitskaya, O.V.5    Panchenko, A.R.6
  • 11
    • 33750999318 scopus 로고    scopus 로고
    • Disorder and sequence repeats in hub proteins and their implications for network evolution
    • 10.1021/pr060171o, 17081050
    • Dosztányi Z, Chen J, Dunker AK, Simon I, Tompa P. Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res 2006, 5:2985-2995. 10.1021/pr060171o, 17081050.
    • (2006) J Proteome Res , vol.5 , pp. 2985-2995
    • Dosztányi, Z.1    Chen, J.2    Dunker, A.K.3    Simon, I.4    Tompa, P.5
  • 12
    • 48249097986 scopus 로고    scopus 로고
    • Intrinsically disordered proteins in human diseases: introducing the D2 concept
    • 10.1146/annurev.biophys.37.032807.125924, 18573080
    • Uversky VN, Oldfield CJ, Dunker AK. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 2008, 37:215-246. 10.1146/annurev.biophys.37.032807.125924, 18573080.
    • (2008) Annu Rev Biophys , vol.37 , pp. 215-246
    • Uversky, V.N.1    Oldfield, C.J.2    Dunker, A.K.3
  • 13
    • 41449104565 scopus 로고    scopus 로고
    • Prediction of intrinsic disorder and its use in functional proteomics
    • 10.1007/978-1-59745-547-3_5, 18314578
    • Uversky VN, Radivojac P, Iakoucheva LM, Obradovic Z, Dunker AK. Prediction of intrinsic disorder and its use in functional proteomics. Methods Mol. Biol 2007, 408:69-92. 10.1007/978-1-59745-547-3_5, 18314578.
    • (2007) Methods Mol. Biol , vol.408 , pp. 69-92
    • Uversky, V.N.1    Radivojac, P.2    Iakoucheva, L.M.3    Obradovic, Z.4    Dunker, A.K.5
  • 14
    • 79957878205 scopus 로고    scopus 로고
    • Proteins without 3D structure: definition, detection and beyond
    • 10.1093/bioinformatics/btr175, 21493654
    • Orosz F, Ovádi J. Proteins without 3D structure: definition, detection and beyond. Bioinformatics 2011, 27:1449-1454. 10.1093/bioinformatics/btr175, 21493654.
    • (2011) Bioinformatics , vol.27 , pp. 1449-1454
    • Orosz, F.1    Ovádi, J.2
  • 17
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
    • 10.1093/nar/gkl971, 1669775, 17142228
    • Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007, 35:D301-303. 10.1093/nar/gkl971, 1669775, 17142228.
    • (2007) Nucleic Acids Res , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 18
    • 48449101036 scopus 로고    scopus 로고
    • SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
    • 10.1093/nar/gkn237, 2447787, 18463137
    • Brandt BW, Heringa J, Leunissen JAM. SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Res 2008, 36:W255-259. 10.1093/nar/gkn237, 2447787, 18463137.
    • (2008) Nucleic Acids Res , vol.36
    • Brandt, B.W.1    Heringa, J.2    Leunissen, J.A.M.3
  • 19
    • 78149244240 scopus 로고    scopus 로고
    • MOBI: a web server to define and visualize structural mobility in NMR protein ensembles
    • 10.1093/bioinformatics/btq537, 20861031
    • Martin AJM, Walsh I, Tosatto SCE. MOBI: a web server to define and visualize structural mobility in NMR protein ensembles. Bioinformatics 2010, 26:2916-2917. 10.1093/bioinformatics/btq537, 20861031.
    • (2010) Bioinformatics , vol.26 , pp. 2916-2917
    • Martin, A.J.M.1    Walsh, I.2    Tosatto, S.C.E.3
  • 20
    • 84857170967 scopus 로고    scopus 로고
    • ESpritz: accurate and fast prediction of protein disorder
    • 10.1093/bioinformatics/btr682, 22190692
    • Walsh I, Martin AJM, Di Domenico T, Tosatto SCE. ESpritz: accurate and fast prediction of protein disorder. Bioinformatics 2012, 28:503-509. 10.1093/bioinformatics/btr682, 22190692.
    • (2012) Bioinformatics , vol.28 , pp. 503-509
    • Walsh, I.1    Martin, A.J.M.2    Di Domenico, T.3    Tosatto, S.C.E.4
  • 22
    • 82655175485 scopus 로고    scopus 로고
    • A comprehensive overview of computational protein disorder prediction methods
    • 10.1039/c1mb05207a, 3633217, 21874190
    • Deng X, Eickholt J, Cheng J. A comprehensive overview of computational protein disorder prediction methods. Mol Biosyst 2012, 8:114-121. 10.1039/c1mb05207a, 3633217, 21874190.
    • (2012) Mol Biosyst , vol.8 , pp. 114-121
    • Deng, X.1    Eickholt, J.2    Cheng, J.3
  • 24
    • 30344485673 scopus 로고    scopus 로고
    • Exploiting heterogeneous sequence properties improves prediction of protein disorder
    • Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 2005, 61(Suppl 7):176-182.
    • (2005) Proteins , vol.61 , Issue.SUPPL 7 , pp. 176-182
    • Obradovic, Z.1    Peng, K.2    Vucetic, S.3    Radivojac, P.4    Dunker, A.K.5
  • 25
    • 79959956361 scopus 로고    scopus 로고
    • CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs
    • 10.1093/nar/gkr411, 3125791, 21646342
    • Walsh I, Martin AJM, Di Domenico T, Vullo A, Pollastri G, Tosatto SCE. CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. Nucleic Acids Res 2011, 39:W190-196. 10.1093/nar/gkr411, 3125791, 21646342.
    • (2011) Nucleic Acids Res , vol.39
    • Walsh, I.1    Martin, A.J.M.2    Di Domenico, T.3    Vullo, A.4    Pollastri, G.5    Tosatto, S.C.E.6
  • 26
    • 0242458482 scopus 로고    scopus 로고
    • Protein disorder prediction: implications for structural proteomics
    • 10.1016/j.str.2003.10.002, 14604535
    • Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure 2003, 11:1453-1459. 10.1016/j.str.2003.10.002, 14604535.
    • (2003) Structure , vol.11 , pp. 1453-1459
    • Linding, R.1    Jensen, L.J.2    Diella, F.3    Bork, P.4    Gibson, T.J.5    Russell, R.B.6
  • 27
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • 10.1093/bioinformatics/bti541, 15955779
    • Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005, 21:3433-3434. 10.1093/bioinformatics/bti541, 15955779.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztányi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 28
    • 84865129593 scopus 로고    scopus 로고
    • MobiDB: a comprehensive database of intrinsic protein disorder annotations
    • 10.1093/bioinformatics/bts327, 22661649
    • Di Domenico T, Walsh I, Martin AJM, Tosatto SCE. MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics 2012, 28:2080-2081. 10.1093/bioinformatics/bts327, 22661649.
    • (2012) Bioinformatics , vol.28 , pp. 2080-2081
    • Di Domenico, T.1    Walsh, I.2    Martin, A.J.M.3    Tosatto, S.C.E.4
  • 30
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • 3245120, 22102590, The UniProt Consortium
    • The UniProt Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-75. 3245120, 22102590, The UniProt Consortium.
    • (2012) Nucleic Acids Res , vol.40
  • 31
    • 78651316211 scopus 로고    scopus 로고
    • OMA 2011: orthology inference among 1000 complete genomes
    • 10.1093/nar/gkq1238, 3013747, 21113020
    • Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 2011, 39:D289-294. 10.1093/nar/gkq1238, 3013747, 21113020.
    • (2011) Nucleic Acids Res , vol.39
    • Altenhoff, A.M.1    Schneider, A.2    Gonnet, G.H.3    Dessimoz, C.4
  • 36
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • 10.1002/bip.360221211, 6667333
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637. 10.1002/bip.360221211, 6667333.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2


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