-
1
-
-
0042622240
-
GlobPlot: Exploring protein sequences for globularity and disorder
-
R. Linding, R. B. Russell, V. Neduva, T. J. Gibson, GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31, 3701-3708 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3701-3708
-
-
Linding, R.1
Russell, R.B.2
Neduva, V.3
Gibson, T.J.4
-
2
-
-
33644876020
-
Pfam: Clans, web tools and services
-
R. D. Finn, J. Mistry, B. Schuster-Böckler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. Sonnhammer, A. Bateman, Pfam: Clans, web tools and services. Nucleic Acids Res. 34, D247-D251 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Böckler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.12
Bateman, A.13
-
3
-
-
33644877451
-
SMART 5: Domains in the context of genomes and networks
-
I. Letunic, R. R. Copley, B. Pils, S. Pinkert, J. Schultz, P. Bork, SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res. 34, D257-D260 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Letunic, I.1
Copley, R.R.2
Pils, B.3
Pinkert, S.4
Schultz, J.5
Bork, P.6
-
4
-
-
33745957790
-
"Bits" and pieces
-
M. B. Yaffe, "Bits" and pieces. Sci. STKE 2006, pe28 (2006).
-
(2006)
Sci. STKE
, vol.2006
-
-
Yaffe, M.B.1
-
5
-
-
33749535603
-
Co-evolution of transcriptional and posttranslational cell-cycle regulation
-
L. J. Jensen, T. S. Jensen, U. de Lichtenberg, S. Brunak, P. Bork, Co-evolution of transcriptional and posttranslational cell-cycle regulation. Nature 443, 594-597 (2006).
-
(2006)
Nature
, vol.443
, pp. 594-597
-
-
Jensen, L.J.1
Jensen, T.S.2
De Lichtenberg, U.3
Brunak, S.4
Bork, P.5
-
6
-
-
20444414545
-
Linear motifs: Evolutionary interaction switches
-
V. Neduva, R. B. Russell, Linear motifs: Evolutionary interaction switches. FEBS Lett. 579, 3342-3345 (2005).
-
(2005)
FEBS Lett.
, vol.579
, pp. 3342-3345
-
-
Neduva, V.1
Russell, R.B.2
-
7
-
-
44249108848
-
Directional and quantitative phosphorylation networks
-
C. Jørgensen, R. Linding, Directional and quantitative phosphorylation networks. Brief Funct Genomic Proteomic. 7, 17-26 (2008).
-
(2008)
Brief Funct Genomic Proteomic.
, vol.7
, pp. 17-26
-
-
Jørgensen, C.1
Linding, R.2
-
8
-
-
4344574540
-
Large-scale characterization of HeLa cell nuclear phosphoproteins
-
S. A. Beausoleil, M. Jedrychowski, D. Schwartz, J. E. Elias, J. Villen, J. Li, M. A. Cohn, L. C. Cantley, S. P. Gygi, Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U.S.A. 101, 12130-12135 (2004).
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 12130-12135
-
-
Beausoleil, S.A.1
Jedrychowski, M.2
Schwartz, D.3
Elias, J.E.4
Villen, J.5
Li, J.6
Cohn, M.A.7
Cantley, L.C.8
Gygi, S.P.9
-
9
-
-
33750456519
-
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
-
J. V. Olsen, B. Blagoev, F. Gnad, B. Macek, C. Kumar, P. Mortensen, M. Mann, Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 127, 635-648 (2006).
-
(2006)
Cell
, vol.127
, pp. 635-648
-
-
Olsen, J.V.1
Blagoev, B.2
Gnad, F.3
Macek, B.4
Kumar, C.5
Mortensen, P.6
Mann, M.7
-
11
-
-
34250722602
-
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
-
A. Wolf-Yadlin, S. Hautaniemi, D. A. Lauffenburger, F. M. White, Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. U.S.A. 104, 5860-5865 (2007).
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 5860-5865
-
-
Wolf-Yadlin, A.1
Hautaniemi, S.2
Lauffenburger, D.A.3
White, F.M.4
-
12
-
-
34250743173
-
Systematic discovery of in vivo phosphorylation networks
-
R. Linding, L. J. Jensen, G. J. Ostheimer, M. A. van Vugt, C. Jørgensen, I. M. Miron, F. Diella, K. Colwill, L. Taylor, K. Elder, P. Metalnikov, V. Nguyen, A. Pasculescu, J. Jin, J. G. Park, L. D. Samson, J. R. Woodgett, R. B. Russell, P. Bork, M. B. Yaffe, T. Pawson, Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415-1426 (2007).
-
(2007)
Cell
, vol.129
, pp. 1415-1426
-
-
Linding, R.1
Jensen, L.J.2
Ostheimer, G.J.3
Van Vugt, M.A.4
Jørgensen, C.5
Miron, I.M.6
Diella, F.7
Colwill, K.8
Taylor, L.9
Elder, K.10
Metalnikov, P.11
Nguyen, V.12
Pasculescu, A.13
Jin, J.14
Park, J.G.15
Samson, L.D.16
Woodgett, J.R.17
Russell, R.B.18
Bork, P.19
Yaffe, M.B.20
Pawson, T.21
more..
-
13
-
-
0042622251
-
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs
-
J. C. Obenauer, L. C. Cantley, M. B. Yaffe, Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31, 3635-3641 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3635-3641
-
-
Obenauer, J.C.1
Cantley, L.C.2
Yaffe, M.B.3
-
14
-
-
0042622252
-
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
-
P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D. M. Martin, G. Ausiello, B. Brannetti, A. Costantini, F. Ferre, V. Maselli, A. Via, G. Cesareni, F. Diella, G. Superti-Furga, L. Wyrwicz, C. Ramu, C. McGuigan, R. Gudavalli, I. Letunic, P. Bork, L. Rychlewski, B. Kuster, M. Helmer-Citterich, W. N. Hunter, R. Aasland, T. J. Gibson, ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 31, 3625-3630 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3625-3630
-
-
Puntervoll, P.1
Linding, R.2
Gemund, C.3
Chabanis-Davidson, S.4
Mattingsdal, M.5
Cameron, S.6
Martin, D.M.7
Ausiello, G.8
Brannetti, B.9
Costantini, A.10
Ferre, F.11
Maselli, V.12
Via, A.13
Cesareni, G.14
Diella, F.15
Superti-Furga, G.16
Wyrwicz, L.17
Ramu, C.18
McGuigan, C.19
Gudavalli, R.20
Letunic, I.21
Bork, P.22
Rychlewski, L.23
Kuster, B.24
Helmer-Citterich, M.25
Hunter, W.N.26
Aasland, R.27
Gibson, T.J.28
more..
-
15
-
-
0034680838
-
Peptide and protein library screening defines optimal substrate motifs for AKT/PKB
-
T. Obata, M. B. Yaffe, G. G. Leparc, E. T. Piro, H. Maegawa, A. Kashiwagi, R. Kikkawa, L. C. Cantley, Peptide and protein library screening defines optimal substrate motifs for AKT/PKB. J. Biol. Chem. 275, 36108-16115 (2000).
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 36108-116115
-
-
Obata, T.1
Yaffe, M.B.2
Leparc, G.G.3
Piro, E.T.4
Maegawa, H.5
Kashiwagi, A.6
Kikkawa, R.7
Cantley, L.C.8
-
16
-
-
17644391197
-
A rapid method for determining protein kinase phosphorylation specificity
-
J. E. Hutti, E. T. Rarrell, J. D. Chang, D. W. Abbott, P. Storz, A. Toker, L. C. Cantley, B. E. Turk, A rapid method for determining protein kinase phosphorylation specificity. Nat. Methods 1, 27-29 (2004).
-
(2004)
Nat. Methods
, vol.1
, pp. 27-29
-
-
Hutti, J.E.1
Rarrell, E.T.2
Chang, J.D.3
Abbott, D.W.4
Storz, P.5
Toker, A.6
Cantley, L.C.7
Turk, B.E.8
-
17
-
-
1542305566
-
An oriented peptide array library (OPAL) strategy to study protein-protein interactions
-
M. Rodriguez, S. S.-C. Li, J. W. Harper, Z. Songyang, An oriented peptide array library (OPAL) strategy to study protein-protein interactions. J. Biol. Chem. 279, 8802-8807 (2004).
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 8802-8807
-
-
Rodriguez, M.1
Li, S.S.-C.2
Harper, J.W.3
Songyang, Z.4
-
18
-
-
33947103658
-
A curated compendium of phosphorylation motifs
-
R. Amanchy, B. Periaswamy, S. Mathivanan, R. Reddy, S. G. Tattikota, A. Pandey, A curated compendium of phosphorylation motifs. Nat. Biotechnol. 25, 285-286 (2007).
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 285-286
-
-
Amanchy, R.1
Periaswamy, B.2
Mathivanan, S.3
Reddy, R.4
Tattikota, S.G.5
Pandey, A.6
-
19
-
-
38549107891
-
The 20 years of PROSITE
-
N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, B. A. Cuche, E. De Castro, C. Lachaize, P. S. Langendijk-Genevaux, C. J. A. Sigrist, The 20 years of PROSITE. Nucleic Acids Res. 36, D245-D249 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Hulo, N.1
Bairoch, A.2
Bulliard, V.3
Cerutti, L.4
Cuche, B.A.5
De Castro, E.6
Lachaize, C.7
Langendijk-Genevaux, P.S.8
Sigrist, C.J.A.9
-
20
-
-
2942564430
-
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
-
N. Blom, T. Sicheritz-Pontén, R. Gupta, S. Gammeltoft, S. Brunak, Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4, 1633-1649 (2004).
-
(2004)
Proteomics
, vol.4
, pp. 1633-1649
-
-
Blom, N.1
Sicheritz-Pontén, T.2
Gupta, R.3
Gammeltoft, S.4
Brunak, S.5
-
21
-
-
8844219516
-
Prediction of phosphorylation sites using SVMs
-
J. H. Kim, J. Lee, B. Oh, K. Kimm, I. Koh, Prediction of phosphorylation sites using SVMs. Bioinformatics 20, 3179-3184 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 3179-3184
-
-
Kim, J.H.1
Lee, J.2
Oh, B.3
Kimm, K.4
Koh, I.5
-
22
-
-
23144452431
-
GPS: A comprehensive www server for phosphorylation sites prediction
-
Y. Xue, F. Zhou, M. Zhu, K. Ahmed, G. Chen, X. Yao, GPS: A comprehensive www server for phosphorylation sites prediction. Nucleic Acids Res. 33, W184-W187 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Xue, Y.1
Zhou, F.2
Zhu, M.3
Ahmed, K.4
Chen, G.5
Yao, X.6
-
23
-
-
33645758540
-
PPSP: Prediction of PK-specific phosphorylation site with Bayesian decision theory
-
Y. Xue, A. Li, L. Wang, H. Feng, X. Yao, PPSP: Prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics 7, 163 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 163
-
-
Xue, Y.1
Li, A.2
Wang, L.3
Feng, H.4
Yao, X.5
-
24
-
-
34547555987
-
KinasePhos 2.0: A web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
-
Y. H. Wong, T. Y. Lee, H. K. Liang, C. M. Huang, T. Y. Wang, Y. H. Yang, C. H. Chu, H. D. Huang, M. T. Ko, J. K. Hwang, KinasePhos 2.0: A web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 35, W588-W594 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Wong, Y.H.1
Lee, T.Y.2
Liang, H.K.3
Huang, C.M.4
Wang, T.Y.5
Yang, Y.H.6
Chu, C.H.7
Huang, H.D.8
Ko, M.T.9
Hwang, J.K.10
-
25
-
-
0037032835
-
The protein kinase complement of the human genome
-
G. Manning, D. B. Whyte, R. Martinez, T. Hunter, S. Sudarsanam, The protein kinase complement of the human genome. Science 298, 1912-1934 (2002).
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
26
-
-
38549092088
-
Phospho.ELM: A database of phosphorylation sites - update 2008
-
F. Diella, C. M. Gould, C. Chica, A. Via, T. J. Gibson, Phospho.ELM: A database of phosphorylation sites - update 2008. Nucleic Acids Res. 36, D240-D244 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Diella, F.1
Gould, C.M.2
Chica, C.3
Via, A.4
Gibson, T.J.5
-
27
-
-
33846102842
-
DOMINO: A database of domain-peptide interactions
-
A. Ceol, A. Chatr-aryamontri, E. Santonico, R. Sacco, L. Castanogli, G. Cesareni, DOMINO: A database of domain-peptide interactions. Nucleic Acids Res. 35, D557-D560 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Ceol, A.1
Chatr-aryamontri, A.2
Santonico, E.3
Sacco, R.4
Castanogli, L.5
Cesareni, G.6
-
28
-
-
30544449081
-
A quantitative protein interaction network for the ErbB receptors using protein microarrays
-
R. B. Jones, A. Gordus, J. A. Krall, G. MacBeath, A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439, 168-174 (2006).
-
(2006)
Nature
, vol.439
, pp. 168-174
-
-
Jones, R.B.1
Gordus, A.2
Krall, J.A.3
MacBeath, G.4
-
29
-
-
33745185987
-
The human and mouse complement of SH2 domain proteins - establishing the boundaries of phosphotyrosine signaling
-
B. A. Liu, K. Jablonowski, M. Raina, M. Arcé, T. Pawson, P. D. Nash, The human and mouse complement of SH2 domain proteins - establishing the boundaries of phosphotyrosine signaling. Mol. Cell 22, 851-868 (2006).
-
(2006)
Mol. Cell
, vol.22
, pp. 851-868
-
-
Liu, B.A.1
Jablonowski, K.2
Raina, M.3
Arcé, M.4
Pawson, T.5
Nash, P.D.6
-
30
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: An overview
-
P. Baldi, S. Brunak, Y. Chauvin, C. A. F. Andersen, H. Nielsen, Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics 16, 412-424 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.F.4
Nielsen, H.5
-
31
-
-
11344286593
-
MAPKAP kinase-2 is a cell cycle checkpoint kinase that regulates the G2/M transition and S phase progression in response to UV irradiation
-
I. A. Manke, A. Nguyen, D. Lim, M. Q. Stewart, A. E. Elia, M. B. Yaffe, MAPKAP kinase-2 is a cell cycle checkpoint kinase that regulates the G2/M transition and S phase progression in response to UV irradiation. Mol. Cell 17, 37-48 (2005).
-
(2005)
Mol. Cell
, vol.17
, pp. 37-48
-
-
Manke, I.A.1
Nguyen, A.2
Lim, D.3
Stewart, M.Q.4
Elia, A.E.5
Yaffe, M.B.6
-
32
-
-
38949126980
-
What are artificial neural networks?
-
A. Krogh, What are artificial neural networks? Nat. Biotechnol. 26, 195-197 (2008).
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 195-197
-
-
Krogh, A.1
-
33
-
-
42649123723
-
Defining the specificity space of the human SRC homology 2 domain
-
H. Huang, L. Li, C. Wu, D. Schibli, K. Colwill, S. Ma, C. Li, P. Roy, K. Ho, Z. Songyang, T. Pawson, Y. Gao, S. S. Li, Defining the specificity space of the human SRC homology 2 domain. Mol. Cell. Proteomics. 7, 768-784 (2008).
-
(2008)
Mol. Cell. Proteomics.
, vol.7
, pp. 768-784
-
-
Huang, H.1
Li, L.2
Wu, C.3
Schibli, D.4
Colwill, K.5
Ma, S.6
Li, C.7
Roy, P.8
Ho, K.9
Songyang, Z.10
Pawson, T.11
Gao, Y.12
Li, S.S.13
-
34
-
-
84889795645
-
-
The data are available from the Web site
-
The data are available from the NetPhorest Web site (http://netphorest. info).
-
-
-
-
35
-
-
0031809552
-
NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
-
J. E. Hansen, O. Lund, N. Tolstrup, A. A. Gooley, K. L. Williams, S. Brunak, NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj. J. 15, 115-130 (1998).
-
(1998)
Glycoconj. J.
, vol.15
, pp. 115-130
-
-
Hansen, J.E.1
Lund, O.2
Tolstrup, N.3
Gooley, A.A.4
Williams, K.L.5
Brunak, S.6
-
36
-
-
0033044637
-
Machine learning approaches for the prediction of signal peptides and other protein sorting signals
-
H. Nielsen, S. Brunak, G. von Heijne, Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 12, 3-9 (1999).
-
(1999)
Protein Eng.
, vol.12
, pp. 3-9
-
-
Nielsen, H.1
Brunak, S.2
Von Heijne, G.3
-
37
-
-
0037460964
-
Prediction of human protein function according to Gene Ontology categories
-
L. J. Jensen, R. Gupta, H.-H. Stærfeldt, S. Brunak, Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19, 635-642 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 635-642
-
-
Jensen, L.J.1
Gupta, R.2
Stærfeldt, H.-H.3
Brunak, S.4
-
38
-
-
0020083498
-
The meaning and use of the area under a receiver operating characteristic (ROC) curve
-
J. A. Hanley, B. J. McNeil, The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29-36 (1982).
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, J.A.1
McNeil, B.J.2
-
39
-
-
34250878954
-
Mechanisms of specificity in protein phosphorylation
-
A. Ubersax, J. Ferrell, Jr., Mechanisms of specificity in protein phosphorylation. Nat. Rev. Mol. Cell. Biol. 8, 530-541 (2007).
-
(2007)
Nat. Rev. Mol. Cell. Biol.
, vol.8
, pp. 530-541
-
-
Ubersax, A.1
Ferrell Jr., J.2
-
40
-
-
34547154729
-
Activation segment exchange: A common mechanism of kinase autophosphorylation?
-
A. W. Oliver, S. Knapp, L. H. Pearl, Activation segment exchange: A common mechanism of kinase autophosphorylation? Trends Biochem. Sci. 32, 351-356 (2007).
-
(2007)
Trends Biochem. Sci.
, vol.32
, pp. 351-356
-
-
Oliver, A.W.1
Knapp, S.2
Pearl, L.H.3
-
41
-
-
39449119544
-
Dimerization by activation segment exchange reveals a mechanism for kinase auto-phosphorylation
-
A. C. W. Pike, P. Rellos, F. H. Niesen, A. Turnbull, A. W. Oliver, S. A. Parker, B. E. Turk, L. H. Pearl, S. Knapp, Dimerization by activation segment exchange reveals a mechanism for kinase auto-phosphorylation. EMBO J. 27, 704-714 (2008).
-
(2008)
EMBO J.
, vol.27
, pp. 704-714
-
-
Pike, A.C.W.1
Rellos, P.2
Niesen, F.H.3
Turnbull, A.4
Oliver, A.W.5
Parker, S.A.6
Turk, B.E.7
Pearl, L.H.8
Knapp, S.9
-
42
-
-
19344377539
-
Protein interaction networks by proteome peptide scanning
-
C. Landgraf, S. Panni, L. Montecchi-Palazzi, L. Castanogli, J. Schneider-Mergener, R. Volkmer-Engert, G. Cesareni, Protein interaction networks by proteome peptide scanning. PLoS Biol. 2, 94-103 (2004).
-
(2004)
PLoS Biol.
, vol.2
, pp. 94-103
-
-
Landgraf, C.1
Panni, S.2
Montecchi-Palazzi, L.3
Castanogli, L.4
Schneider-Mergener, J.5
Volkmer-Engert, R.6
Cesareni, G.7
-
43
-
-
34548838274
-
Phage display for engineering and analyzing protein interaction interfaces
-
S. S. Sidhu, S. Koide, Phage display for engineering and analyzing protein interaction interfaces. Curr. Opin. Struct. Biol. 17, 481-487 (2007).
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 481-487
-
-
Sidhu, S.S.1
Koide, S.2
-
44
-
-
34249778657
-
A semisynthetic epitope for kinase substrates
-
J. J. Allen, M. Li, C. S. Brinkworth, J. L. Paulson, D.Wang, A. Hübner, W.-H. Chou, R. J. Davis, A. L. Burlingame, R. O. Messing, C. D. Katayama, S. M. Hedrick, K. M. Shokat, A semisynthetic epitope for kinase substrates. Nat. Methods 4, 511-516 (2007).
-
(2007)
Nat. Methods
, vol.4
, pp. 511-516
-
-
Allen, J.J.1
Li, M.2
Brinkworth, C.S.3
Paulson, J.L.4
Wang, D.5
Hübner, A.6
Chou, W.-H.7
Davis, R.J.8
Burlingame, A.L.9
Messing, R.O.10
Katayama, C.D.11
Hedrick, S.M.12
Shokat, K.M.13
-
45
-
-
34249947699
-
ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
-
S. Matsuoka, B. A. Ballif, A. Smogorzewska, E. R. McDonald III, K. E. Hurov, J. Luo, C. E. Bakalarski, Z. Zhao, N. Solimini, Y. Lerenthal, Y. Shiloh, S. P. Gygi, S. J. Elledge, ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160-1166 (2007).
-
(2007)
Science
, vol.316
, pp. 1160-1166
-
-
Matsuoka, S.1
Ballif, B.A.2
Smogorzewska, A.3
McDonald III, E.R.4
Hurov, K.E.5
Luo, J.6
Bakalarski, C.E.7
Zhao, Z.8
Solimini, N.9
Lerenthal, Y.10
Shiloh, Y.11
Gygi, S.P.12
Elledge, S.J.13
-
46
-
-
34249885757
-
Engineering synthetic signaling proteins with ultrasensitive input/output control
-
J. E. Dueber, E. A. Mirsky, W. A. Lim, Engineering synthetic signaling proteins with ultrasensitive input/output control. Net. Biotechnol. 25, 660-662 (2007).
-
(2007)
Net. Biotechnol.
, vol.25
, pp. 660-662
-
-
Dueber, J.E.1
Mirsky, E.A.2
Lim, W.A.3
-
47
-
-
38549086310
-
Pepcyber:P∼PEP: A database of human protein protein interactions mediated by phosphoprotein-binding domains
-
W. Gong, D. Zhou, Y. Ren, Y. Wang, Z. Zuo, Y. Shen, F.Xiao, Q. Zhu, A. Hong, X. Zhou, X. Gao, T. Li, Pepcyber:P∼PEP: A database of human protein protein interactions mediated by phosphoprotein-binding domains. Nucleic Acids Res. 36, D679-D683 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gong, W.1
Zhou, D.2
Ren, Y.3
Wang, Y.4
Zuo, Z.5
Shen, Y.6
Xiao, F.7
Zhu, Q.8
Hong, A.9
Zhou, X.10
Gao, X.11
Li, T.12
-
48
-
-
33746905531
-
Phosphotyrosine interactome of the ErbB-receptor kinase family
-
W. X. Schulze, L. Deng, M. Mann, Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol. Syst. Biol. 1, 2005.0008 (2005).
-
(2005)
Mol. Syst. Biol.
, vol.1
-
-
Schulze, W.X.1
Deng, L.2
Mann, M.3
-
49
-
-
33750987920
-
Screening for PTB domain binding partners and ligand specificity using proteome-derived NPXY peptide arrays
-
M. J. Smith, W. R. Hardy, J. M. Murphy, N. Jones, T. Pawson, Screening for PTB domain binding partners and ligand specificity using proteome-derived NPXY peptide arrays. Mol. Cell. Biol. 26, 8461-8474 (2006).
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 8461-8474
-
-
Smith, M.J.1
Hardy, W.R.2
Murphy, J.M.3
Jones, N.4
Pawson, T.5
-
50
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
K. Katoh, K. Kuma, H. Toh, T. Miyata, MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511-518 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
51
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
G. Talavera, J. Castresana, Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577 (2007).
-
(2007)
Syst. Biol.
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
52
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
S. Guindon, O. Gascuel, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704 (2003).
-
(2003)
Syst. Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
53
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
W. Li, A. Godzik, Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
54
-
-
0033579464
-
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
-
N. Blom, S. Gammeltoft, S. Brunak, Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294, 1351-1362 (1999).
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 1351-1362
-
-
Blom, N.1
Gammeltoft, S.2
Brunak, S.3
-
55
-
-
0033743209
-
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
-
T. Rognes, E. Seeberg, Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics 16, 699-706 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 699-706
-
-
Rognes, T.1
Seeberg, E.2
-
56
-
-
1542515338
-
A census of human cancer genes
-
P. A. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman, M. R. Stratton, A census of human cancer genes. Nat. Rev. Cancer. 4, 177-183 (2004).
-
(2004)
Nat. Rev. Cancer.
, vol.4
, pp. 177-183
-
-
Futreal, P.A.1
Coin, L.2
Marshall, M.3
Down, T.4
Hubbard, T.5
Wooster, R.6
Rahman, N.7
Stratton, M.R.8
-
57
-
-
38549109487
-
A resource for exploring cellular phosphorylation networks
-
R. Linding, L. J. Jensen, A. Pasculescu, M. Olhovsky, K. Colwill, P. Bork, M. B. Yaffe, T. Pawson, NetworKIN: A resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 36, D695-D699 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Linding, R.1
Jensen, L.J.2
Pasculescu, A.3
Olhovsky, M.4
Colwill, K.5
Bork, P.6
Yaffe, M.B.7
Pawson, T.8
Networ, K.I.N.9
-
58
-
-
33847616949
-
Reproducible isolation of distinct, overlapping segments of the phosphoproteome
-
B. Bodenmiller, L. N. Mueller, M. Mueller, B. Domon, R. Aebersold, Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods 4, 231-237 (2007).
-
(2007)
Nat Methods
, vol.4
, pp. 231-237
-
-
Bodenmiller, B.1
Mueller, L.N.2
Mueller, M.3
Domon, B.4
Aebersold, R.5
|