-
2
-
-
0028859279
-
Protein modules and signalling networks
-
Pawson T (1995) Protein modules and signalling networks. Nature 373(6515):573-580
-
(1995)
Nature
, vol.373
, Issue.6515
, pp. 573-580
-
-
Pawson, T.1
-
3
-
-
0019336436
-
The mechanism of protein secretion across membranes
-
Davis BD, Tai PC (1980) The mechanism of protein secretion across membranes. Nature 283(5746):433-438
-
(1980)
Nature
, vol.283
, Issue.5746
, pp. 433-438
-
-
Davis, B.D.1
Tai, P.C.2
-
4
-
-
18344376699
-
Normalization of nomenclature for peptide motifs as ligands of modular protein domains
-
Aasland R, Abrams C, Ampe C et al (2002) Normalization of nomenclature for peptide motifs as ligands of modular protein domains. FEBS Lett 513(1):141-144
-
(2002)
FEBS Lett
, vol.513
, Issue.1
, pp. 141-144
-
-
Aasland, R.1
Abrams, C.2
Ampe, C.3
-
5
-
-
0042622252
-
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
-
Puntervoll P, Linding R, Gemund C et al (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31(13):3625-3630
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3625-3630
-
-
Puntervoll, P.1
Linding, R.2
Gemund, C.3
-
6
-
-
84861327457
-
Interactions via intrinsically disordered regions: what kind of motifs?
-
Pancsa R, Fuxreiter M (2012) Interactions via intrinsically disordered regions: what kind of motifs? IUBMB Life 64(6):513-520
-
(2012)
IUBMB Life
, vol.64
, Issue.6
, pp. 513-520
-
-
Pancsa, R.1
Fuxreiter, M.2
-
7
-
-
33748953868
-
Peptides mediating interaction networks: new leads at last
-
Neduva V, Russell RB (2006) Peptides mediating interaction networks: new leads at last. Curr Opin Biotechnol 17(5):465-471
-
(2006)
Curr Opin Biotechnol
, vol.17
, Issue.5
, pp. 465-471
-
-
Neduva, V.1
Russell, R.B.2
-
8
-
-
49549122501
-
Understanding eukaryotic linear motifs and their role in cell signaling and regulation
-
Diella F, Haslam N, Chica C et al (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580-6603
-
(2008)
Front Biosci
, vol.13
, pp. 6580-6603
-
-
Diella, F.1
Haslam, N.2
Chica, C.3
-
9
-
-
84891752434
-
The eukaryotic linear motif resource ELM:10 years and counting
-
Dinkel H, Van Roey K, Michael S et al (2014) The eukaryotic linear motif resource ELM:10 years and counting. Nucleic Acids Res 42(1):D259-D266
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.1
, pp. D259-D266
-
-
Dinkel, H.1
Van Roey, K.2
Michael, S.3
-
10
-
-
84859219888
-
Minimotif Miner 3.0: database expansion and significantly improved reduction of falsepositive predictions from consensus sequences
-
(Database issue)
-
Mi T, Merlin JC, Deverasetty S et al (2012) Minimotif Miner 3.0: database expansion and significantly improved reduction of falsepositive predictions from consensus sequences. Nucleic Acids Res 40(Database issue):D252-D260
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D252-D260
-
-
Mi, T.1
Merlin, J.C.2
Deverasetty, S.3
-
11
-
-
77956636245
-
Computational identification and analysis of protein short linear motifs
-
Davey NE, Edwards RJ, Shields DC (2010) Computational identification and analysis of protein short linear motifs. Front Biosci (Landmark Ed) 15:801-825
-
(2010)
Front Biosci (Landmark Ed)
, vol.15
, pp. 801-825
-
-
Davey, N.E.1
Edwards, R.J.2
Shields, D.C.3
-
12
-
-
20444414545
-
Linear motifs:evolutionary interaction switches
-
Neduva V, Russell RB (2005) Linear motifs:evolutionary interaction switches. FEBS Lett 579(15):3342-3345
-
(2005)
FEBS Lett
, vol.579
, Issue.15
, pp. 3342-3345
-
-
Neduva, V.1
Russell, R.B.2
-
14
-
-
69249216579
-
A proposed syntax for Minimotif Semantics, version 1
-
Vyas J, Nowling RJ, Maciejewski MW et al (2009) A proposed syntax for Minimotif Semantics, version 1. BMC Genomics 10:360
-
(2009)
BMC Genomics
, vol.10
, pp. 360
-
-
Vyas, J.1
Nowling, R.J.2
Maciejewski, M.W.3
-
16
-
-
84892876722
-
Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks
-
Garamszegi S, Franzosa EA, Xia Y (2013) Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. PLoS Pathog 9(12):e1003778
-
(2013)
PLoS Pathog
, vol.9
, Issue.12
, pp. e1003778
-
-
Garamszegi, S.1
Franzosa, E.A.2
Xia, Y.3
-
17
-
-
76749168997
-
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins
-
Davey NE, Edwards RJ, Shields DC (2010) Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinform 11:14
-
(2010)
BMC Bioinform
, vol.11
, pp. 14
-
-
Davey, N.E.1
Edwards, R.J.2
Shields, D.C.3
-
18
-
-
0001290045
-
PROSITE: a documented database using patterns and profiles as motif descriptors
-
Sigrist CJ, Cerutti L, Hulo N et al (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3(3):265-274
-
(2002)
Brief Bioinform
, vol.3
, Issue.3
, pp. 265-274
-
-
Sigrist, C.J.1
Cerutti, L.2
Hulo, N.3
-
19
-
-
84901319636
-
Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction
-
Xia X (2012) Position weight matrix, gibbs sampler, and the associated significance tests in motif characterization and prediction. Scientifica (Cairo) 2012:917540
-
(2012)
Scientifica (Cairo)
, vol.2012
, pp. 917540
-
-
Xia, X.1
-
20
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14(9):755-763
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
22
-
-
0042622251
-
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
-
Obenauer JC, Cantley LC, Yaffe MB (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31(13):3635-3641
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3635-3641
-
-
Obenauer, J.C.1
Cantley, L.C.2
Yaffe, M.B.3
-
23
-
-
70549108054
-
Hidden Markov models and their applications in biological sequence analysis
-
Yoon BJ (2009) Hidden Markov models and their applications in biological sequence analysis. Curr Genomics 10(6):402-415
-
(2009)
Curr Genomics
, vol.10
, Issue.6
, pp. 402-415
-
-
Yoon, B.J.1
-
24
-
-
33745071297
-
The 3of5 web application for complex and comprehensive pattern matching in protein sequences
-
Seiler M, Mehrle A, Poustka A et al (2006) The 3of5 web application for complex and comprehensive pattern matching in protein sequences. BMC Bioinform 7:144
-
(2006)
BMC Bioinform
, vol.7
, pp. 144
-
-
Seiler, M.1
Mehrle, A.2
Poustka, A.3
-
25
-
-
78049486947
-
SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context
-
Davey NE, Haslam NJ, Shields DC et al (2010) SLiMSearch: a webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context. Lect Notes Bioinform 6282:50-61
-
(2010)
Lect Notes Bioinform
, vol.6282
, pp. 50-61
-
-
Davey, N.E.1
Haslam, N.J.2
Shields, D.C.3
-
26
-
-
84867055643
-
Disordered binding regions and linear motifs-bridging the gap between two models of molecular recognition
-
Meszaros B, Dosztanyi Z, Simon I (2012) Disordered binding regions and linear motifs-bridging the gap between two models of molecular recognition. PLoS One 7(10):e46829
-
(2012)
PLoS One
, vol.7
, Issue.10
, pp. e46829
-
-
Meszaros, B.1
Dosztanyi, Z.2
Simon, I.3
-
27
-
-
60149099647
-
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
-
Davey NE, Shields DC, Edwards RJ (2009) Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics 25(4):443-450
-
(2009)
Bioinformatics
, vol.25
, Issue.4
, pp. 443-450
-
-
Davey, N.E.1
Shields, D.C.2
Edwards, R.J.3
-
28
-
-
0036017388
-
Evolutionary rate heterogeneity in proteins with long disordered regions
-
Brown CJ, Takayama S, Campen AM et al (2002) Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 55(1):104-110
-
(2002)
J Mol Evol
, vol.55
, Issue.1
, pp. 104-110
-
-
Brown, C.J.1
Takayama, S.2
Campen, A.M.3
-
29
-
-
58149144095
-
Assessing conservation of disordered regions in proteins
-
Tóth-Petróczy A, Mészáros B, Simon I et al (2008) Assessing conservation of disordered regions in proteins. Open Proteom J 1:46-53
-
(2008)
Open Proteom J
, vol.1
, pp. 46-53
-
-
Tóth-Petróczy, A.1
Mészáros, B.2
Simon, I.3
-
30
-
-
34249695447
-
Local structural disorder imparts plasticity on linear motifs
-
Fuxreiter M, Tompa P, Simon I (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23(8):950-956
-
(2007)
Bioinformatics
, vol.23
, Issue.8
, pp. 950-956
-
-
Fuxreiter, M.1
Tompa, P.2
Simon, I.3
-
31
-
-
33746300776
-
Proteinprotein interaction through beta-strand addition
-
Remaut H, Waksman G (2006) Proteinprotein interaction through beta-strand addition. Trends Biochem Sci 31(8):436-444
-
(2006)
Trends Biochem Sci
, vol.31
, Issue.8
, pp. 436-444
-
-
Remaut, H.1
Waksman, G.2
-
32
-
-
84890904756
-
Conformational biases of linear motifs
-
Cino EA, Choy WY, Karttunen M (2013) Conformational biases of linear motifs. J Phys Chem B 117(50):15943-15957
-
(2013)
J Phys Chem B
, vol.117
, Issue.50
, pp. 15943-15957
-
-
Cino, E.A.1
Choy, W.Y.2
Karttunen, M.3
-
33
-
-
58149147308
-
Disordered flanks prevent peptide aggregation
-
Abeln S, Frenkel D (2008) Disordered flanks prevent peptide aggregation. PLoS Comput Biol 4(12):e1000241
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.12
, pp. e1000241
-
-
Abeln, S.1
Frenkel, D.2
-
34
-
-
84857618740
-
SiteBinder: an improved approach for comparing multiple protein structural motifs
-
Sehnal D, Varekova RS, Huber HJ et al (2012) SiteBinder: an improved approach for comparing multiple protein structural motifs. J Chem Inf Model 52(2):343-359
-
(2012)
J Chem Inf Model
, vol.52
, Issue.2
, pp. 343-359
-
-
Sehnal, D.1
Varekova, R.S.2
Huber, H.J.3
-
35
-
-
84862992463
-
Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
-
Buljan M, Chalancon G, Eustermann S et al (2012) Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 46(6):871-883
-
(2012)
Mol Cell
, vol.46
, Issue.6
, pp. 871-883
-
-
Buljan, M.1
Chalancon, G.2
Eustermann, S.3
-
36
-
-
84863928687
-
Linear motifs confer functional diversity onto splice variants
-
Weatheritt RJ, Davey NE, Gibson TJ (2012) Linear motifs confer functional diversity onto splice variants. Nucleic Acids Res 40(15):7123-7131
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.15
, pp. 7123-7131
-
-
Weatheritt, R.J.1
Davey, N.E.2
Gibson, T.J.3
-
37
-
-
84864311086
-
Linear motifs: lost in (pre)translation
-
Weatheritt RJ, Gibson TJ (2012) Linear motifs: lost in (pre)translation. Trends Biochem Sci 37(8):333-341
-
(2012)
Trends Biochem Sci
, vol.37
, Issue.8
, pp. 333-341
-
-
Weatheritt, R.J.1
Gibson, T.J.2
-
38
-
-
84891798215
-
TISdb: a database for alternative translation initiation in mammalian cells
-
Wan J, Qian SB (2014) TISdb: a database for alternative translation initiation in mammalian cells. Nucleic Acids Res 42(1):D845-D850
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.1
, pp. D845-D850
-
-
Wan, J.1
Qian, S.B.2
-
39
-
-
46049107404
-
Alternative translation start sites and hidden coding potential of eukaryotic mRNAs
-
Kochetov AV (2008) Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays 30(7):683-691
-
(2008)
Bioessays
, vol.30
, Issue.7
, pp. 683-691
-
-
Kochetov, A.V.1
-
40
-
-
84891783174
-
Activities at the universal protein resource (UniProt)
-
UniProt C (2014) Activities at the universal protein resource (UniProt). Nucleic Acids Res 42(1):D191-D198
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.1
, pp. D191-D198
-
-
UniProt, C.1
-
41
-
-
41149120313
-
SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins
-
Edwards RJ, Davey NE, Shields DC (2007) SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS One 2(10):e967
-
(2007)
PLoS One
, vol.2
, Issue.10
, pp. e967
-
-
Edwards, R.J.1
Davey, N.E.2
Shields, D.C.3
-
42
-
-
34547588388
-
The SLiMDisc server: short, linear motif discovery in proteins
-
(Web Server issue)
-
Davey NE, Edwards RJ, Shields DC (2007) The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res 35(Web Server issue):W455-W459
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W455-W459
-
-
Davey, N.E.1
Edwards, R.J.2
Shields, D.C.3
-
44
-
-
24944546549
-
Coupled folding and binding with alpha-helix-forming molecular recognition elements
-
Oldfield CJ, Cheng Y, Cortese MS et al (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44(37): 12454-12470
-
(2005)
Biochemistry
, vol.44
, Issue.37
, pp. 12454-12470
-
-
Oldfield, C.J.1
Cheng, Y.2
Cortese, M.S.3
-
45
-
-
33748456399
-
Analysis of molecular recognition features (MoRFs)
-
Mohan A, Oldfield CJ, Radivojac P et al (2006) Analysis of molecular recognition features (MoRFs). J Mol Biol 362(5):1043-1059
-
(2006)
J Mol Biol
, vol.362
, Issue.5
, pp. 1043-1059
-
-
Mohan, A.1
Oldfield, C.J.2
Radivojac, P.3
-
46
-
-
34250815165
-
Characterization of molecular recognition features, MoRFs, and their binding partners
-
Vacic V, Oldfield CJ, Mohan A et al (2007) Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res 6(6):2351-2366
-
(2007)
J Proteome Res
, vol.6
, Issue.6
, pp. 2351-2366
-
-
Vacic, V.1
Oldfield, C.J.2
Mohan, A.3
-
47
-
-
49749117432
-
Contextual specificity in peptide-mediated protein interactions
-
Stein A, Aloy P (2008) Contextual specificity in peptide-mediated protein interactions. PLoS One 3(7):e2524
-
(2008)
PLoS One
, vol.3
, Issue.7
, pp. e2524
-
-
Stein, A.1
Aloy, P.2
-
48
-
-
84864612979
-
Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains
-
Teyra J, Sidhu SS, Kim PM (2012) Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains. FEBS Lett 586(17):2631-2637
-
(2012)
FEBS Lett
, vol.586
, Issue.17
, pp. 2631-2637
-
-
Teyra, J.1
Sidhu, S.S.2
Kim, P.M.3
-
49
-
-
80455129692
-
Yeast two-hybrid junk sequences contain selected linear motifs
-
Liu Y, Woods NT, Kim D et al (2011) Yeast two-hybrid junk sequences contain selected linear motifs. Nucleic Acids Res 39(19):e128
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.19
, pp. e128
-
-
Liu, Y.1
Woods, N.T.2
Kim, D.3
-
50
-
-
77952778270
-
Prediction of posttranslational modification of proteins from their amino acid sequence
-
Eisenhaber B, Eisenhaber F (2010) Prediction of posttranslational modification of proteins from their amino acid sequence. Methods Mol Biol 609:365-384
-
(2010)
Methods Mol Biol
, vol.609
, pp. 365-384
-
-
Eisenhaber, B.1
Eisenhaber, F.2
-
51
-
-
80054937592
-
Computational prediction of eukaryotic phosphorylation sites
-
Trost B, Kusalik A (2011) Computational prediction of eukaryotic phosphorylation sites. Bioinformatics 27(21):2927-2935
-
(2011)
Bioinformatics
, vol.27
, Issue.21
, pp. 2927-2935
-
-
Trost, B.1
Kusalik, A.2
-
52
-
-
27744585113
-
ProRule: a new database containing functional and structural information on PROSITE profiles
-
Sigrist CJ, De Castro E, Langendijk-Genevaux PS et al (2005) ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics 21(21):4060-4066
-
(2005)
Bioinformatics
, vol.21
, Issue.21
, pp. 4060-4066
-
-
Sigrist, C.J.1
De Castro, E.2
Langendijk-Genevaux, P.S.3
-
53
-
-
84876588470
-
New and continuing developments at PROSITE
-
(Database issue)
-
Sigrist CJ, de Castro E, Cerutti L et al (2013) New and continuing developments at PROSITE. Nucleic Acids Res 41(Database issue):D344-D347
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D344-D347
-
-
Sigrist, C.J.1
de Castro, E.2
Cerutti, L.3
-
54
-
-
84862221167
-
SMART 7: recent updates to the protein domain annotation resource
-
(Database issue)
-
Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40(Database issue):D302-D305
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D302-D305
-
-
Letunic, I.1
Doerks, T.2
Bork, P.3
-
55
-
-
84858077472
-
The Pfam protein families database
-
(Database issue)
-
Punta M, Coggill PC, Eberhardt RY et al (2012) The Pfam protein families database. Nucleic Acids Res 40(Database issue):D290-D301
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D290-D301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
-
56
-
-
43249115776
-
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
-
Chica C, Labarga A, Gould CM et al (2008) A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinform 9:229
-
(2008)
BMC Bioinform
, vol.9
, pp. 229
-
-
Chica, C.1
Labarga, A.2
Gould, C.M.3
-
57
-
-
71749106147
-
A structure filter for the Eukaryotic Linear Motif Resource
-
Via A, Gould CM, Gemund C et al (2009) A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinform 10:351
-
(2009)
BMC Bioinform
, vol.10
, pp. 351
-
-
Via, A.1
Gould, C.M.2
Gemund, C.3
-
58
-
-
84864465529
-
iELM-a web server to explore short linear motif-mediated interactions
-
(Web Server issue)
-
Weatheritt RJ, Jehl P, Dinkel H et al (2012) iELM-a web server to explore short linear motif-mediated interactions. Nucleic Acids Res 40(Web Server issue):W364-W369
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W364-W369
-
-
Weatheritt, R.J.1
Jehl, P.2
Dinkel, H.3
-
59
-
-
78651320816
-
Phospho.ELM: a database of phosphorylation sites-update 2011
-
(Database issue)
-
Dinkel H, Chica C, Via A et al (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res 39(Database issue):D261-D267
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D261-D267
-
-
Dinkel, H.1
Chica, C.2
Via, A.3
-
60
-
-
84876158670
-
The switches.ELM resource: a compendium of conditional regulatory interaction interfaces
-
Van Roey K, Dinkel H, Weatheritt RJ et al (2013) The switches.ELM resource: a compendium of conditional regulatory interaction interfaces. Sci Signal 6(269):rs7
-
(2013)
Sci Signal
, vol.6
, Issue.269
, pp. rs7
-
-
Van Roey, K.1
Dinkel, H.2
Weatheritt, R.J.3
-
61
-
-
84865103448
-
Modular evolution of phosphorylation-based signalling systems
-
Jin J, Pawson T (2012) Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 367(1602):2540-2555
-
(2012)
Philos Trans R Soc Lond B Biol Sci
, vol.367
, Issue.1602
, pp. 2540-2555
-
-
Jin, J.1
Pawson, T.2
-
62
-
-
0028540405
-
Use of an oriented peptide library to determine the optimal substrates of protein kinases
-
Songyang Z, Blechner S, Hoagland N et al (1994) Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 4(11):973-982
-
(1994)
Curr Biol
, vol.4
, Issue.11
, pp. 973-982
-
-
Songyang, Z.1
Blechner, S.2
Hoagland, N.3
-
63
-
-
82655175473
-
Interactome-wide prediction of short, disordered protein interaction motifs in humans
-
Edwards RJ, Davey NE, O'Brien K et al (2012) Interactome-wide prediction of short, disordered protein interaction motifs in humans. Mol Biosyst 8(1):282-295
-
(2012)
Mol Biosyst
, vol.8
, Issue.1
, pp. 282-295
-
-
Edwards, R.J.1
Davey, N.E.2
O'Brien, K.3
-
65
-
-
0033985936
-
Online mendelian inheritance in man (OMIM)
-
Hamosh A, Scott AF, Amberger J et al (2000) Online mendelian inheritance in man (OMIM). Hum Mutat 15(1):57-61
-
(2000)
Hum Mutat
, vol.15
, Issue.1
, pp. 57-61
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.3
-
66
-
-
84855658379
-
Human protein reference database and human proteinpedia as resources for phosphoproteome analysis
-
Goel R, Harsha HC, Pandey A et al (2012) Human protein reference database and human proteinpedia as resources for phosphoproteome analysis. Mol Biosyst 8(2):453-463
-
(2012)
Mol Biosyst
, vol.8
, Issue.2
, pp. 453-463
-
-
Goel, R.1
Harsha, H.C.2
Pandey, A.3
-
67
-
-
78049480691
-
GeneCards Version 3: the human gene integrator
-
(Oxford), baq020
-
Safran M, Dalah I, Alexander J et al (2010) GeneCards Version 3: the human gene integrator. Database (Oxford) 2010:baq020
-
Database
-
-
Safran, M.1
Dalah, I.2
Alexander, J.3
-
68
-
-
79959984707
-
SLiMSearch 2.0: biological context for short linear motifs in proteins
-
(Web Server issue)
-
Davey NE, Haslam NJ, Shields DC et al (2011) SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res 39(Web Server issue):W56-W60
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W56-W60
-
-
Davey, N.E.1
Haslam, N.J.2
Shields, D.C.3
-
69
-
-
43349092663
-
CompariMotif: quick and easy comparisons of sequence motifs
-
Edwards RJ, Davey NE, Shields DC (2008) CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics 24(10):1307-1309
-
(2008)
Bioinformatics
, vol.24
, Issue.10
, pp. 1307-1309
-
-
Edwards, R.J.1
Davey, N.E.2
Shields, D.C.3
-
70
-
-
75549084896
-
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins
-
(Database issue)
-
Marsico A, Scheubert K, Tuukkanen A et al (2010) MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. Nucleic Acids Res 38(Database issue):D181-D189
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D181-D189
-
-
Marsico, A.1
Scheubert, K.2
Tuukkanen, A.3
-
71
-
-
29144455315
-
Systematic discovery of new recognition peptides mediating protein interaction networks
-
Neduva V, Linding R, Su-Angrand I et al (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 3(12):e405
-
(2005)
PLoS Biol
, vol.3
, Issue.12
, pp. e405
-
-
Neduva, V.1
Linding, R.2
Su-Angrand, I.3
-
72
-
-
67849122320
-
MEME SUITE: tools for motif discovery and searching
-
(Web Server issue)
-
Bailey TL, Boden M, Buske FA et al (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37(Web Server issue):W202-W208
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
-
73
-
-
79953300078
-
FIMO: scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27(7):1017-1018
-
(2011)
Bioinformatics
, vol.27
, Issue.7
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
74
-
-
44949239504
-
Discovering sequence motifs with arbitrary insertions and deletions
-
Frith MC, Saunders NF, Kobe B et al (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol 4(4):e1000071
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.4
, pp. e1000071
-
-
Frith, M.C.1
Saunders, N.F.2
Kobe, B.3
-
75
-
-
0030965735
-
Score distributions for simultaneous matching to multiple motifs
-
Bailey TL, Gribskov M (1997) Score distributions for simultaneous matching to multiple motifs. J Comput Biol 4(1):45-59
-
(1997)
J Comput Biol
, vol.4
, Issue.1
, pp. 45-59
-
-
Bailey, T.L.1
Gribskov, M.2
-
76
-
-
33747839468
-
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
-
(Web Server issue)
-
de Castro E, Sigrist CJ, Gattiker A et al (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34(Web Server issue):W362-W365
-
(2006)
Nucleic Acids Res
, vol.34
, pp. W362-W365
-
-
de Castro, E.1
Sigrist, C.J.2
Gattiker, A.3
-
77
-
-
33746812318
-
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
-
Davey NE, Shields DC, Edwards RJ (2006) SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res 34(12):3546-3554
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.12
, pp. 3546-3554
-
-
Davey, N.E.1
Shields, D.C.2
Edwards, R.J.3
-
78
-
-
84857129811
-
Comprehensive comparative assessment of in-silico predictors of disordered regions
-
Peng ZL, Kurgan L (2012) Comprehensive comparative assessment of in-silico predictors of disordered regions. Curr Protein Pept Sci 13(1):6-18
-
(2012)
Curr Protein Pept Sci
, vol.13
, Issue.1
, pp. 6-18
-
-
Peng, Z.L.1
Kurgan, L.2
-
79
-
-
82655175485
-
A comprehensive overview of computational protein disorder prediction methods
-
Deng X, Eickholt J, Cheng J (2012) A comprehensive overview of computational protein disorder prediction methods. Mol Biosyst 8(1):114-121
-
(2012)
Mol Biosyst
, vol.8
, Issue.1
, pp. 114-121
-
-
Deng, X.1
Eickholt, J.2
Cheng, J.3
-
80
-
-
24044538903
-
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
-
Dosztanyi Z, Csizmok V, Tompa P et al (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21(16):3433-3434
-
(2005)
Bioinformatics
, vol.21
, Issue.16
, pp. 3433-3434
-
-
Dosztanyi, Z.1
Csizmok, V.2
Tompa, P.3
-
81
-
-
84861175619
-
Profile-based short linear protein motif discovery
-
Haslam NJ, Shields DC (2012) Profile-based short linear protein motif discovery. BMC Bioinform 13:104
-
(2012)
BMC Bioinform
, vol.13
, pp. 104
-
-
Haslam, N.J.1
Shields, D.C.2
-
82
-
-
33846099868
-
DisProt: the database of disordered proteins
-
(Database issue)
-
Sickmeier M, Hamilton JA, LeGall T et al (2007) DisProt: the database of disordered proteins. Nucleic Acids Res 35(Database issue):D786-D793
-
(2007)
Nucleic Acids Res
, vol.35
, pp. D786-D793
-
-
Sickmeier, M.1
Hamilton, J.A.2
LeGall, T.3
-
84
-
-
65249102824
-
Close encounters of the third kind:disordered domains and the interactions of proteins
-
Tompa P, Fuxreiter M, Oldfield CJ et al (2009) Close encounters of the third kind:disordered domains and the interactions of proteins. Bioessays 31(3):328-335
-
(2009)
Bioessays
, vol.31
, Issue.3
, pp. 328-335
-
-
Tompa, P.1
Fuxreiter, M.2
Oldfield, C.J.3
-
85
-
-
84901294912
-
Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains
-
Williams RW, Xue B, Uversky VN et al (2013) Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains. Intrins Disord Prot 1:e25724
-
(2013)
Intrins Disord Prot
, vol.1
, pp. e25724
-
-
Williams, R.W.1
Xue, B.2
Uversky, V.N.3
-
86
-
-
78650524534
-
Generation of a consensus protein domain dictionary
-
Schaeffer RD, Jonsson AL, Simms AM et al (2011) Generation of a consensus protein domain dictionary. Bioinformatics 27(1):46-54
-
(2011)
Bioinformatics
, vol.27
, Issue.1
, pp. 46-54
-
-
Schaeffer, R.D.1
Jonsson, A.L.2
Simms, A.M.3
-
87
-
-
84869123655
-
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative
-
Towse CL, Daggett V (2012) When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. Bioessays 34(12):1060-1069
-
(2012)
Bioessays
, vol.34
, Issue.12
, pp. 1060-1069
-
-
Towse, C.L.1
Daggett, V.2
-
88
-
-
0042622240
-
GlobPlot: exploring protein sequences for globularity and disorder
-
Linding R, Russell RB, Neduva V et al (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res 31(13):3701-3708
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3701-3708
-
-
Linding, R.1
Russell, R.B.2
Neduva, V.3
-
89
-
-
84891779335
-
3did: a catalog of domain-based interactions of known three-dimensional structure
-
Mosca R, Ceol A, Stein A et al (2014) 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 42(1):D374-D379
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.1
, pp. D374-D379
-
-
Mosca, R.1
Ceol, A.2
Stein, A.3
-
90
-
-
77955476975
-
Novel peptidemediated interactions derived from highresolution 3-dimensional structures
-
Stein A, Aloy P (2010) Novel peptidemediated interactions derived from highresolution 3-dimensional structures. PLoS Comput Biol 6(5):e1000789
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.5
, pp. e1000789
-
-
Stein, A.1
Aloy, P.2
-
91
-
-
0041620239
-
iSPOT: a web tool to infer the interaction specificity of families of protein modules
-
Brannetti B, Helmer-Citterich M (2003) iSPOT: a web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Res 31(13):3709-3711
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3709-3711
-
-
Brannetti, B.1
Helmer-Citterich, M.2
-
92
-
-
84864419151
-
PepSite: prediction of peptide-binding sites from protein surfaces
-
(Web Server issue)
-
Trabuco LG, Lise S, Petsalaki E et al (2012) PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res 40(Web Server issue):W423-W427
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W423-W427
-
-
Trabuco, L.G.1
Lise, S.2
Petsalaki, E.3
-
93
-
-
43249091570
-
A new protein linear motif benchmark for multiple sequence alignment software
-
Perrodou E, Chica C, Poch O et al (2008) A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinform 9:213
-
(2008)
BMC Bioinform
, vol.9
, pp. 213
-
-
Perrodou, E.1
Chica, C.2
Poch, O.3
-
94
-
-
78651310799
-
Database resources of the National Center for Biotechnology Information
-
(Database issue)
-
Sayers EW, Barrett T, Benson DA et al (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 39(Database issue):D38-D51
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D38-D51
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
-
95
-
-
33646358251
-
Minimotif Miner: a tool for investigating protein function
-
Balla S, Thapar V, Verma S et al (2006) Minimotif Miner: a tool for investigating protein function. Nat Methods 3(3):175-177
-
(2006)
Nat Methods
, vol.3
, Issue.3
, pp. 175-177
-
-
Balla, S.1
Thapar, V.2
Verma, S.3
-
96
-
-
36949023994
-
A computational strategy for the prediction of functional linear peptide motifs in proteins
-
Dinkel H, Sticht H (2007) A computational strategy for the prediction of functional linear peptide motifs in proteins. Bioinformatics 23(24):3297-3303
-
(2007)
Bioinformatics
, vol.23
, Issue.24
, pp. 3297-3303
-
-
Dinkel, H.1
Sticht, H.2
-
97
-
-
84870600202
-
SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
-
Davey NE, Cowan JL, Shields DC et al (2012) SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Res 40(21):10628-10641
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.21
, pp. 10628-10641
-
-
Davey, N.E.1
Cowan, J.L.2
Shields, D.C.3
-
98
-
-
75849140545
-
Evidence for the concerted evolution between short linear protein motifs and their flanking regions
-
Chica C, Diella F, Gibson TJ (2009) Evidence for the concerted evolution between short linear protein motifs and their flanking regions. PLoS One 4(7):e6052
-
(2009)
PLoS One
, vol.4
, Issue.7
, pp. e6052
-
-
Chica, C.1
Diella, F.2
Gibson, T.J.3
-
99
-
-
84880084863
-
SLiMScape: a protein short linear motif analysis plugin for Cytoscape
-
O'Brien KT, Haslam NJ, Shields DC (2013) SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC Bioinform 14:224
-
(2013)
BMC Bioinform
, vol.14
, pp. 224
-
-
O'Brien, K.T.1
Haslam, N.J.2
Shields, D.C.3
-
100
-
-
77954267294
-
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
-
(Web Server issue)
-
Davey NE, Haslam NJ, Shields DC et al (2010) SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res 38(Web Server issue):W534-W539
-
(2010)
Nucleic Acids Res
, vol.38
, pp. W534-W539
-
-
Davey, N.E.1
Haslam, N.J.2
Shields, D.C.3
-
101
-
-
84864743678
-
AMS 4.0: consensus prediction of post-translational modifications in protein sequences
-
Plewczynski D, Basu S, Saha I (2012) AMS 4.0: consensus prediction of post-translational modifications in protein sequences. Amino Acids 43(2):573-582
-
(2012)
Amino Acids
, vol.43
, Issue.2
, pp. 573-582
-
-
Plewczynski, D.1
Basu, S.2
Saha, I.3
-
102
-
-
84859204939
-
The IntAct molecular interaction database in 2012
-
Database issue
-
Kerrien S, Aranda B, Breuza L et al (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40(Database issue):D841-D846
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D841-D846
-
-
Kerrien, S.1
Aranda, B.2
Breuza, L.3
-
103
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
104
-
-
33947389235
-
False occurrences of functional motifs in protein sequences highlight evolutionary constraints
-
Via A, Gherardini PF, Ferraro E et al (2007) False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinform 8:68
-
(2007)
BMC Bioinform
, vol.8
, pp. 68
-
-
Via, A.1
Gherardini, P.F.2
Ferraro, E.3
-
105
-
-
84858267844
-
Proteome-wide discovery of evolutionary conserved sequences in disordered regions
-
Nguyen Ba AN, Yeh BJ, van Dyk D et al (2012) Proteome-wide discovery of evolutionary conserved sequences in disordered regions. Sci Signal 5(215):rs1
-
(2012)
Sci Signal
, vol.5
, Issue.215
, pp. rs1
-
-
Nguyen Ba, A.N.1
Yeh, B.J.2
van Dyk, D.3
-
106
-
-
84884959977
-
MFSPSSMpred: identifying short disorderto-order binding regions in disordered proteins based on contextual local evolutionary conservation
-
Fang C, Noguchi T, Tominaga D et al (2013) MFSPSSMpred: identifying short disorderto-order binding regions in disordered proteins based on contextual local evolutionary conservation. BMC Bioinform 14:300
-
(2013)
BMC Bioinform
, vol.14
, pp. 300
-
-
Fang, C.1
Noguchi, T.2
Tominaga, D.3
-
107
-
-
84857518627
-
Biological sequence motif discovery using motif-x
-
Chou MF, Schwartz D (2011) Biological sequence motif discovery using motif-x . Curr Protoc Bioinform Chapter 13, Unit 13 15-24
-
(2011)
, pp. 15-24
-
-
Chou, M.F.1
Schwartz, D.2
-
108
-
-
84862642360
-
Molecular interaction databases
-
Orchard S (2012) Molecular interaction databases. Proteomics 12(10):1656-1662
-
(2012)
Proteomics
, vol.12
, Issue.10
, pp. 1656-1662
-
-
Orchard, S.1
-
109
-
-
0030670589
-
Efficient discovery of conserved patterns using a pattern graph
-
Jonassen I (1997) Efficient discovery of conserved patterns using a pattern graph. Comput Appl Biosci 13(5):509-522
-
(1997)
Comput Appl Biosci
, vol.13
, Issue.5
, pp. 509-522
-
-
Jonassen, I.1
-
110
-
-
0029159799
-
Finding flexible patterns in unaligned protein sequences
-
Jonassen I, Collins JF, Higgins DG (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci 4(8):1587-1595
-
(1995)
Protein Sci
, vol.4
, Issue.8
, pp. 1587-1595
-
-
Jonassen, I.1
Collins, J.F.2
Higgins, D.G.3
-
111
-
-
0028270992
-
Detecting patterns in protein sequences
-
Neuwald AF, Green P (1994) Detecting patterns in protein sequences. J Mol Biol 239(5):698-712
-
(1994)
J Mol Biol
, vol.239
, Issue.5
, pp. 698-712
-
-
Neuwald, A.F.1
Green, P.2
-
112
-
-
0031684427
-
Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm
-
Rigoutsos I, Floratos A (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14(1):55-67
-
(1998)
Bioinformatics
, vol.14
, Issue.1
, pp. 55-67
-
-
Rigoutsos, I.1
Floratos, A.2
-
113
-
-
33747824163
-
DILIMOT:discovery of linear motifs in proteins
-
Web Server issue
-
Neduva V, Russell RB (2006) DILIMOT:discovery of linear motifs in proteins. Nucleic Acids Res 34(Web Server issue):W350-W355
-
(2006)
Nucleic Acids Res
, vol.34
, pp. W350-W355
-
-
Neduva, V.1
Russell, R.B.2
-
114
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28-36
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
115
-
-
0025320805
-
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
Lawrence CE, Reilly AA (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 7(1):41-51
-
(1990)
Proteins
, vol.7
, Issue.1
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
116
-
-
49449098182
-
What is the expectation maximization algorithm?
-
Do CB, Batzoglou S (2008) What is the expectation maximization algorithm? Nat Biotechnol 26(8):897-899
-
(2008)
Nat Biotechnol
, vol.26
, Issue.8
, pp. 897-899
-
-
Do, C.B.1
Batzoglou, S.2
-
117
-
-
14944363825
-
NestedMICA:sensitive inference of over-represented motifs in nucleic acid sequence
-
Down TA, Hubbard TJ (2005) NestedMICA:sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res 33(5):1445-1453
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.5
, pp. 1445-1453
-
-
Down, T.A.1
Hubbard, T.J.2
-
118
-
-
41149162675
-
NestedMICA as an ab initio protein motif discovery tool
-
Dogruel M, Down TA, Hubbard TJ (2008) NestedMICA as an ab initio protein motif discovery tool. BMC Bioinform 9:19
-
(2008)
BMC Bioinform
, vol.9
, pp. 19
-
-
Dogruel, M.1
Down, T.A.2
Hubbard, T.J.3
-
119
-
-
84891857502
-
PMS: a panoptic motif search tool
-
Dinh H, Rajasekaran S (2013) PMS: a panoptic motif search tool. PLoS One 8(12):e80660
-
(2013)
PLoS One
, vol.8
, Issue.12
, pp. e80660
-
-
Dinh, H.1
Rajasekaran, S.2
-
120
-
-
84864189089
-
qPMS7: a fast algorithm for finding (l, d)-motifs in DNA and protein sequences
-
Dinh H, Rajasekaran S, Davila J (2012) qPMS7: a fast algorithm for finding (l, d)-motifs in DNA and protein sequences. PLoS One 7(7):e41425
-
(2012)
PLoS One
, vol.7
, Issue.7
, pp. e41425
-
-
Dinh, H.1
Rajasekaran, S.2
Davila, J.3
-
121
-
-
33845276720
-
A correlated motif approach for finding short linear motifs from protein interaction networks
-
Tan SH, Hugo W, Sung WK et al (2006) A correlated motif approach for finding short linear motifs from protein interaction networks. BMC Bioinform 7:502
-
(2006)
BMC Bioinform
, vol.7
, pp. 502
-
-
Tan, S.H.1
Hugo, W.2
Sung, W.K.3
-
122
-
-
68349110569
-
Clustering-based approach for predicting motif pairs from protein interaction data
-
Leung HC, Siu MH, Yiu SM et al (2009) Clustering-based approach for predicting motif pairs from protein interaction data. J Bioinform Comput Biol 7(4):701-716
-
(2009)
J Bioinform Comput Biol
, vol.7
, Issue.4
, pp. 701-716
-
-
Leung, H.C.1
Siu, M.H.2
Yiu, S.M.3
-
123
-
-
79953904499
-
SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks
-
Boyen P, Van Dyck D, Neven F et al (2011) SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks. IEEE/ACM Trans Comput Biol Bioinform 8(5):1344-1357
-
(2011)
IEEE/ACM Trans Comput Biol Bioinform
, vol.8
, Issue.5
, pp. 1344-1357
-
-
Boyen, P.1
Van Dyck, D.2
Neven, F.3
-
124
-
-
78650821937
-
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes
-
Lieber DS, Elemento O, Tavazoie S (2010) Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One 5(12):e14444
-
(2010)
PLoS One
, vol.5
, Issue.12
, pp. e14444
-
-
Lieber, D.S.1
Elemento, O.2
Tavazoie, S.3
-
125
-
-
70349996473
-
ANCHOR: web server for predicting protein binding regions in disordered proteins
-
Dosztanyi Z, Meszaros B, Simon I (2009) ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics 25(20):2745-2746
-
(2009)
Bioinformatics
, vol.25
, Issue.20
, pp. 2745-2746
-
-
Dosztanyi, Z.1
Meszaros, B.2
Simon, I.3
-
126
-
-
67049119327
-
Prediction of protein binding regions in disordered proteins
-
Meszaros B, Simon I, Dosztanyi Z (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput Biol 5(5):e1000376
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.5
, pp. e1000376
-
-
Meszaros, B.1
Simon, I.2
Dosztanyi, Z.3
-
127
-
-
36749037699
-
Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
-
Cheng Y, Oldfield CJ, Meng J et al (2007) Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 46(47):13468-13477
-
(2007)
Biochemistry
, vol.46
, Issue.47
, pp. 13468-13477
-
-
Cheng, Y.1
Oldfield, C.J.2
Meng, J.3
-
128
-
-
84863518014
-
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
-
Disfani FM, Hsu WL, Mizianty MJ et al (2012) MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics 28(12):i75-i83
-
(2012)
Bioinformatics
, vol.28
, Issue.12
, pp. i75-i83
-
-
Disfani, F.M.1
Hsu, W.L.2
Mizianty, M.J.3
-
129
-
-
84855278383
-
Prediction of short linear protein binding regions
-
Mooney C, Pollastri G, Shields DC et al (2012) Prediction of short linear protein binding regions. J Mol Biol 415(1):193-204
-
(2012)
J Mol Biol
, vol.415
, Issue.1
, pp. 193-204
-
-
Mooney, C.1
Pollastri, G.2
Shields, D.C.3
-
130
-
-
84876529328
-
The RCSB Protein Data Bank: new resources for research and education
-
Database issue
-
Rose PW, Bi C, Bluhm WF et al (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res 41(Database issue):D475-D482
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D475-D482
-
-
Rose, P.W.1
Bi, C.2
Bluhm, W.F.3
-
131
-
-
34848835475
-
Structure-templated predictions of novel protein interactions from sequence information
-
Betel D, Breitkreuz KE, Isserlin R et al (2007) Structure-templated predictions of novel protein interactions from sequence information. PLoS Comput Biol 3(9):1783-1789
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.9
, pp. 1783-1789
-
-
Betel, D.1
Breitkreuz, K.E.2
Isserlin, R.3
-
132
-
-
84871868863
-
Discovering interacting domains and motifs in protein-protein interactions
-
Hugo W, Sung WK, Ng SK (2013) Discovering interacting domains and motifs in protein-protein interactions. Methods Mol Biol 939:9-20
-
(2013)
Methods Mol Biol
, vol.939
, pp. 9-20
-
-
Hugo, W.1
Sung, W.K.2
Ng, S.K.3
-
133
-
-
70349308508
-
Cell regulation: determined to signal discrete cooperation
-
Gibson TJ (2009) Cell regulation: determined to signal discrete cooperation. Trends Biochem Sci 34(10):471-482
-
(2009)
Trends Biochem Sci
, vol.34
, Issue.10
, pp. 471-482
-
-
Gibson, T.J.1
-
134
-
-
77951969848
-
MOTIPS: automated motif analysis for predicting targets of modular protein domains
-
Lam HY, Kim PM, Mok J et al (2010) MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinform 11:243
-
(2010)
BMC Bioinform
, vol.11
, pp. 243
-
-
Lam, H.Y.1
Kim, P.M.2
Mok, J.3
-
135
-
-
27944499451
-
An iterative statistical approach to the identification of protein phosphorylation motifs from largescale data sets
-
Schwartz D, Gygi SP (2005) An iterative statistical approach to the identification of protein phosphorylation motifs from largescale data sets. Nat Biotechnol 23(11):1391-1398
-
(2005)
Nat Biotechnol
, vol.23
, Issue.11
, pp. 1391-1398
-
-
Schwartz, D.1
Gygi, S.P.2
-
136
-
-
61649126270
-
Predicting protein post-translational modifi-cations using meta-analysis of proteome scale data sets
-
Schwartz D, Chou MF, Church GM (2009) Predicting protein post-translational modifi-cations using meta-analysis of proteome scale data sets. Mol Cell Proteomics 8(2):365-379
-
(2009)
Mol Cell Proteomics
, vol.8
, Issue.2
, pp. 365-379
-
-
Schwartz, D.1
Chou, M.F.2
Church, G.M.3
-
139
-
-
45549086908
-
Phosphoproteome analysis of Drosophila melanogaster embryos
-
Zhai B, Villen J, Beausoleil SA et al (2008) Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res 7(4):1675-1682
-
(2008)
J Proteome Res
, vol.7
, Issue.4
, pp. 1675-1682
-
-
Zhai, B.1
Villen, J.2
Beausoleil, S.A.3
-
140
-
-
84955146443
-
-
[cited 25/1/14]; Available from
-
Edwards RJ. SLiMSuite software package. 2013 [cited 25/1/14]; Available from:http://www.southampton.ac.uk/~re1u06/software/packages/slimsuite/
-
(2013)
SLiMSuite software package
-
-
Edwards, R.J.1
|