-
1
-
-
0037250158
-
InterPreTS: Protein Interaction Prediction through Tertiary Structure
-
DOI 10.1093/bioinformatics/19.1.161
-
Aloy P, Russell RB (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19: 161-162 (Pubitemid 36150198)
-
(2003)
Bioinformatics
, vol.19
, Issue.1
, pp. 161-162
-
-
Aloy, P.1
Russell, R.B.2
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57: 289-300
-
(1995)
J R Stat Soc ser B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
4
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
5
-
-
78650632764
-
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
-
Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R et al (2010) Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal 3: rs4
-
(2010)
Sci Signal
, vol.3
-
-
Bodenmiller, B.1
Wanka, S.2
Kraft, C.3
Urban, J.4
Campbell, D.5
Pedrioli, P.G.6
Gerrits, B.7
Picotti, P.8
Lam, H.9
Vitek, O.10
Brusniak, M.Y.11
Roschitzki, B.12
Zhang, C.13
Shokat, K.M.14
Schlapbach, R.15
Colman-Lerner, A.16
Nolan, G.P.17
Nesvizhskii, A.I.18
Peter, M.19
Loewith, R.20
more..
-
6
-
-
64749108158
-
Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
-
Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ (2009) Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 4: 484-494
-
(2009)
Nat Protoc
, vol.4
, pp. 484-494
-
-
Boersema, P.J.1
Raijmakers, R.2
Lemeer, S.3
Mohammed, S.4
Heck, A.J.5
-
7
-
-
40749141227
-
OutlierD: An R package for outlier detection using quantile regression on mass spectrometry data
-
DOI 10.1093/bioinformatics/btn012
-
ChoH,Kim YJ, Jung HJ, Lee SW, LeeJW(2008) OutlierD:anR package for outlier detection using quantile regression on mass spectrometry data. Bioinformatics 24: 882-884 (Pubitemid 351386936)
-
(2008)
Bioinformatics
, vol.24
, Issue.6
, pp. 882-884
-
-
Cho, H.1
Kim, Y.-J.2
Jung, H.J.3
Lee, S.-W.4
Lee, J.W.5
-
8
-
-
68949212379
-
Lysine acetylation targets protein complexes and co-regulates major cellular functions
-
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325: 834-840
-
(2009)
Science
, vol.325
, pp. 834-840
-
-
Choudhary, C.1
Kumar, C.2
Gnad, F.3
Nielsen, M.L.4
Rehman, M.5
Walther, T.C.6
Olsen, J.V.7
Mann, M.8
-
9
-
-
78651319979
-
Ongoing and future developments at the Universal Protein Resource
-
UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214-D219
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Consortium, U.1
-
10
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
11
-
-
0034284160
-
Re-annotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames
-
Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, DoerksT, Sanchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P (2000) Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res 28: 3278-3288 (Pubitemid 30662292)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.17
, pp. 3278-3288
-
-
Dandekar, T.1
Huynen, M.2
Regula, J.T.3
Ueberle, B.4
Zimmermann, C.U.5
Andrade, M.A.6
Doerks, T.7
Sanchez-Pulido, L.8
Snel, B.9
Suyama, M.10
Yuan, Y.P.11
Herrmann, R.12
Bork, P.13
-
12
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
DOI 10.1126/science.1105103
-
de Lichtenberg U, Jensen LJ, Brunak S, Bork P (2005) Dynamic complex formation during the yeast cell cycle. Science 307: 724-727 (Pubitemid 40194642)
-
(2005)
Science
, vol.307
, Issue.5710
, pp. 724-727
-
-
De Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
Bork, P.4
-
13
-
-
77953292595
-
Post-translational modifications in signal integration
-
Deribe YL, Pawson T, Dikic I (2010) Post-translational modifications in signal integration. Nat Struct Mol Biol 17: 666-672
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 666-672
-
-
Deribe, Y.L.1
Pawson, T.2
Dikic, I.3
-
14
-
-
78651320816
-
Phospho.ELM: A database of phosphorylation sites-update 2011
-
Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res 39: D261-D267
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Dinkel, H.1
Chica, C.2
Via, A.3
Gould, C.M.4
Jensen, L.J.5
Gibson, T.J.6
Diella, F.7
-
15
-
-
78651277460
-
PHOSIDA 2011: The posttranslational modification database
-
Gnad F, Gunawardena J, Mann M (2011) PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res 39: D253-D260
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Gnad, F.1
Gunawardena, J.2
Mann, M.3
-
16
-
-
70849119931
-
Transcriptome complexity in a genome-reduced bacterium
-
Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kuhner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271
-
(2009)
Science
, vol.326
, pp. 1268-1271
-
-
Guell, M.1
Van Noort, V.2
Yus, E.3
Chen, W.H.4
Leigh-Bell, J.5
Michalodimitrakis, K.6
Yamada, T.7
Arumugam, M.8
Doerks, T.9
Kuhner, S.10
Rode, M.11
Suyama, M.12
Schmidt, S.13
Gavin, A.C.14
Bork, P.15
Serrano, L.16
-
17
-
-
33748755047
-
Regulatory protein phosphorylation in Mycoplasma pneumoniae: A PP2C-type phosphatase serves to dephosphorylate HPr(Ser-P)
-
DOI 10.1074/jbc.M605010200
-
Halbedel S, Busse J, Schmidl SR, Stulke J (2006) Regulatory protein phosphorylation in Mycoplasma pneumoniae. A PP2C-type phosphatase serves to dephosphorylate HPr(Ser-P). J Biol Chem 281: 26253-26259 (Pubitemid 44401833)
-
(2006)
Journal of Biological Chemistry
, vol.281
, Issue.36
, pp. 26253-26259
-
-
Halbedel, S.1
Busse, J.2
Schmidl, S.R.3
Stulke, J.4
-
18
-
-
33748989006
-
Transposon mutagenesis identifies genes associated with Mycoplasma pneumoniae gliding motility
-
DOI 10.1128/JB.00698-06
-
Hasselbring BM, Page CA, Sheppard ES, Krause DC (2006) Transposon mutagenesis identifies genes associated with Mycoplasma pneumoniae gliding motility. J Bacteriol 188: 6335-6345 (Pubitemid 44448576)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.17
, pp. 6335-6345
-
-
Hasselbring, B.M.1
Page, C.A.2
Sheppard, E.S.3
Krause, D.C.4
-
19
-
-
24944475661
-
Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase
-
DOI 10.1016/j.jmb.2005.07.042, PII S0022283605008430
-
Hible G, Renault L, Schaeffer F, Christova P, Zoe Radulescu A, Evrin C, Gilles AM, Cherfils J (2005) Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J Mol Biol 352: 1044-1059 (Pubitemid 41316714)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.5
, pp. 1044-1059
-
-
Hible, G.1
Renault, L.2
Schaeffer, F.3
Christova, P.4
Radulescu, A.Z.5
Evrin, C.6
Gilles, A.-M.7
Cherfils, J.8
-
20
-
-
2942598149
-
PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation
-
DOI 10.1002/pmic.200300772
-
Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B (2004) PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics 4: 1551-1561 (Pubitemid 38738314)
-
(2004)
Proteomics
, vol.4
, Issue.6
, pp. 1551-1561
-
-
Hornbeck, P.V.1
Chabra, I.2
Kornhauser, J.M.3
Skrzypek, E.4
Zhang, B.5
-
21
-
-
77954013335
-
Bacterial protein acetylation: The dawning of a new age
-
Hu LI, Lima BP, Wolfe AJ (2010) Bacterial protein acetylation: the dawning of a new age. Mol Microbiol 77: 15-21
-
(2010)
Mol Microbiol
, vol.77
, pp. 15-21
-
-
Hu, L.I.1
Lima, B.P.2
Wolfe, A.J.3
-
22
-
-
78650466243
-
A tissue-specific atlas of mouse protein phosphorylation and expression
-
Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP (2010) A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143: 1174-1189
-
(2010)
Cell
, vol.143
, pp. 1174-1189
-
-
Huttlin, E.L.1
Jedrychowski, M.P.2
Elias, J.E.3
Goswami, T.4
Rad, R.5
Beausoleil, S.A.6
Villen, J.7
Haas, W.8
Sowa, M.E.9
Gygi, S.P.10
-
23
-
-
0942287072
-
Proteogenomic mapping as a complementary method to perform genome annotation
-
DOI 10.1002/pmic.200300511
-
Jaffe JD, Berg HC, Church GM (2004) Proteogenomic mapping as a complementary methodtoperform genome annotation. Proteomics 4: 59-77 (Pubitemid 38140875)
-
(2004)
Proteomics
, vol.4
, Issue.1
, pp. 59-77
-
-
Jaffe, J.D.1
Berg, H.C.2
Church, G.M.3
-
24
-
-
58149193234
-
STRING 8 - A global view on proteins and their functional interactions in 630 organisms
-
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37: D412-D416
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Jensen, L.J.1
Kuhn, M.2
Stark, M.3
Chaffron, S.4
Creevey, C.5
Muller, J.6
Doerks, T.7
Julien, P.8
Roth, A.9
Simonovic, M.10
Bork, P.11
Von Mering, C.12
-
25
-
-
0035839136
-
Translating the histone code
-
DOI 10.1126/science.1063127
-
Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080 (Pubitemid 32758077)
-
(2001)
Science
, vol.293
, Issue.5532
, pp. 1074-1080
-
-
Jenuwein, T.1
Allis, C.D.2
-
26
-
-
0033953802
-
Autophosphorylation of phosphoglucosamine mutase from Escherichia coli
-
DOI 10.1128/JB.182.5.1280-1285.2000
-
Jolly L, Pompeo F, van Heijenoort J, Fassy F, Mengin-Lecreulx D (2000) Autophosphorylation of phosphoglucosamine mutase from Escherichia coli. J Bacteriol 182: 1280-1285 (Pubitemid 30104404)
-
(2000)
Journal of Bacteriology
, vol.182
, Issue.5
, pp. 1280-1285
-
-
Jolly, L.1
Pompeo, F.2
Van Heijenoort, J.3
Fassy, F.4
Mengin-Lecreulx, D.5
-
27
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
DOI 10.1038/nmeth1113, PII NMETH1113
-
Kall L, Canterbury JD, Weston J, Noble WS, MacCoss MJ (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4: 923-925 (Pubitemid 350042380)
-
(2007)
Nature Methods
, vol.4
, Issue.11
, pp. 923-925
-
-
Kall, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
28
-
-
0030025671
-
The structure of the Escherichia coli EF-Tu.EF-Ts complex at 2.5 A resolution
-
Kawashima T, Berthet-Colominas C, Wulff M, Cusack S, Leberman R (1996) The structure of the Escherichia coli EF-Tu.EF-Ts complex at 2.5 A resolution. Nature 379: 511-518
-
(1996)
Nature
, vol.379
, pp. 511-518
-
-
Kawashima, T.1
Berthet-Colominas, C.2
Wulff, M.3
Cusack, S.4
Leberman, R.5
-
29
-
-
0037005989
-
Protein kinases and protein phosphatases in prokaryotes: A genomic perspective
-
DOI 10.1016/S0378-1097(01)00479-7, PII S0378109701004797
-
Kennelly PJ (2002) Protein kinases and protein phosphatases in prokaryotes: a genomic perspective. FEMS Microbiol Lett 206: 1-8 (Pubitemid 34084930)
-
(2002)
FEMS Microbiology Letters
, vol.206
, Issue.1
, pp. 1-8
-
-
Kennelly, P.J.1
-
30
-
-
33746992118
-
Substrate and Functional Diversity of Lysine Acetylation Revealed by a Proteomics Survey
-
DOI 10.1016/j.molcel.2006.06.026, PII S1097276506004540
-
Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, Cheng T, Kho Y, Xiao H, Xiao L, Grishin NV, White M, Yang XJ, Zhao Y (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23: 607-618 (Pubitemid 44205490)
-
(2006)
Molecular Cell
, vol.23
, Issue.4
, pp. 607-618
-
-
Kim, S.C.1
Sprung, R.2
Chen, Y.3
Xu, Y.4
Ball, H.5
Pei, J.6
Cheng, T.7
Kho, Y.8
Xiao, H.9
Xiao, L.10
Grishin, N.V.11
White, M.12
Yang, X.-J.13
Zhao, Y.14
-
31
-
-
70849132924
-
Proteome organization in a genome-reduced bacterium
-
Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castano-Diez D, Chen WH, Devos D, Guell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R et al (2009) Proteome organization in a genome-reduced bacterium. Science 326: 1235-1240
-
(2009)
Science
, vol.326
, pp. 1235-1240
-
-
Kuhner, S.1
Van Noort, V.2
Betts, M.J.3
Leo-Macias, A.4
Batisse, C.5
Rode, M.6
Yamada, T.7
Maier, T.8
Bader, S.9
Beltran-Alvarez, P.10
Castano-Diez, D.11
Chen, W.H.12
Devos, D.13
Guell, M.14
Norambuena, T.15
Racke, I.16
Rybin, V.17
Schmidt, A.18
Yus, E.19
Aebersold, R.20
more..
-
32
-
-
71049118572
-
SysPTM: A systematic resource for proteomic research on post-translational modifications
-
Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y (2009) SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol Cell Proteomics 8: 1839-1849
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 1839-1849
-
-
Li, H.1
Xing, X.2
Ding, G.3
Li, Q.4
Wang, C.5
Xie, L.6
Zeng, R.7
Li, Y.8
-
33
-
-
39749166860
-
Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
-
DOI 10.1074/mcp.M700311-MCP200
-
Macek B, Gnad F, Soufi B, Kumar C, Olsen JV, Mijakovic I, Mann M (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol Cell Proteomics 7: 299-307 (Pubitemid 351298444)
-
(2008)
Molecular and Cellular Proteomics
, vol.7
, Issue.2
, pp. 299-307
-
-
Macek, B.1
Gnad, F.2
Soufi, B.3
Kumar, C.4
Olsen, J.V.5
Mijakovic, I.6
Mann, M.7
-
34
-
-
34247325212
-
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
-
DOI 10.1074/mcp.M600464-MCP200
-
Macek B, Mijakovic I, Olsen JV, Gnad F, Kumar C, Jensen PR, Mann M (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 6: 697-707 (Pubitemid 46630102)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.4
, pp. 697-707
-
-
Macek, B.1
Mijakovic, I.2
Olsen, J.V.3
Gnad, F.4
Kumar, C.5
Jensen, P.R.6
Mann, M.7
-
35
-
-
79960578471
-
Quantification of mRNA and protein and integration with protein turnover in a bacterium
-
Maier T, Schmidt A, Guell M, Kuhner S, Gavin AC, Aebersold R, Serrano L (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7: 511
-
(2011)
Mol Syst Biol
, vol.7
, pp. 511
-
-
Maier, T.1
Schmidt, A.2
Guell, M.3
Kuhner, S.4
Gavin, A.C.5
Aebersold, R.6
Serrano, L.7
-
36
-
-
33645466839
-
Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine
-
Mijakovic I, Petranovic D, Macek B, Cepo T, Mann M, Davies J, Jensen PR, Vujaklija D (2006) Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine. Nucleic Acids Res 34: 1588-1596
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1588-1596
-
-
Mijakovic, I.1
Petranovic, D.2
MacEk, B.3
Cepo, T.4
Mann, M.5
Davies, J.6
Jensen, P.R.7
Vujaklija, D.8
-
37
-
-
79551536399
-
Strong cation exchange (SCX) based analytical methods for the targeted analysis of protein post-translational modifications
-
Mohammed S, Heck AJ (2010) Strong cation exchange (SCX) based analytical methods for the targeted analysis of protein post-translational modifications. Curr Opin Biotechnol 22: 9-16
-
(2010)
Curr Opin Biotechnol
, vol.22
, pp. 9-16
-
-
Mohammed, S.1
Heck, A.J.2
-
38
-
-
73649131275
-
MSQuant, an open source platform for mass spectrometry-based quantitative proteomics
-
Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, Cox J, Foster LJ, Heck AJ, Blagoev B, Andersen JS, Mann M (2010) MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res 9: 393-403
-
(2010)
J Proteome Res
, vol.9
, pp. 393-403
-
-
Mortensen, P.1
Gouw, J.W.2
Olsen, J.V.3
Ong, S.E.4
Rigbolt, K.T.5
Bunkenborg, J.6
Cox, J.7
Foster, L.J.8
Heck, A.J.9
Blagoev, B.10
Andersen, J.S.11
Mann, M.12
-
39
-
-
75549085495
-
EggNOG v2.0: Extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
-
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P (2010) eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 38: D190-D195
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Muller, J.1
Szklarczyk, D.2
Julien, P.3
Letunic, I.4
Roth, A.5
Kuhn, M.6
Powell, S.7
Von Mering, C.8
Doerks, T.9
Jensen, L.J.10
Bork, P.11
-
40
-
-
79957932347
-
Crystal structure of the maltose transporter in a pretranslocation intermediate state
-
Oldham ML, Chen J (2011) Crystal structure of the maltose transporter in a pretranslocation intermediate state. Science 332: 1202-1205
-
(2011)
Science
, vol.332
, pp. 1202-1205
-
-
Oldham, M.L.1
Chen, J.2
-
41
-
-
58149187896
-
MODBASE, a database of annotated comparative protein structure models and associated resources
-
PieperU,Eswar N,Webb BM, Eramian D, KellyL, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A (2009) MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 37: D347-D354
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Pieper, U.1
Eswar, N.2
Webb, B.M.3
Eramian, D.4
Kelly, L.5
Barkan, D.T.6
Carter, H.7
Mankoo, P.8
Karchin, R.9
Marti-Renom, M.A.10
Davis, F.P.11
Sali, A.12
-
42
-
-
77952132933
-
Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
-
Prisic S, Dankwa S, Schwartz D, Chou MF, Locasale JW, Kang CM, Bemis G, Church GM, Steen H, Husson RN (2010) Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci USA 107: 7521-7526
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 7521-7526
-
-
Prisic, S.1
Dankwa, S.2
Schwartz, D.3
Chou, M.F.4
Locasale, J.W.5
Kang, C.M.6
Bemis, G.7
Church, G.M.8
Steen, H.9
Husson, R.N.10
-
43
-
-
34548183872
-
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
-
DOI 10.1038/nprot.2007.261, PII NPROT.2007.261
-
Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2: 1896-1906 (Pubitemid 47308128)
-
(2007)
Nature Protocols
, vol.2
, Issue.8
, pp. 1896-1906
-
-
Rappsilber, J.1
Mann, M.2
Ishihama, Y.3
-
44
-
-
33750618516
-
Microtubule acetylation promotes kinesin-1 binding and transport
-
DOI 10.1016/j.cub.2006.09.014, PII S096098220602207X
-
Reed NA, Cai D, Blasius TL, Jih GT, Meyhofer E, Gaertig J, Verhey KJ (2006) Microtubule acetylation promotes kinesin-1 binding and transport. Curr Biol 16: 2166-2172 (Pubitemid 44692098)
-
(2006)
Current Biology
, vol.16
, Issue.21
, pp. 2166-2172
-
-
Reed, N.A.1
Cai, D.2
Blasius, T.L.3
Jih, G.T.4
Meyhofer, E.5
Gaertig, J.6
Verhey, K.J.7
-
45
-
-
79952752375
-
System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation
-
Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B (2011) System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal 4: rs3
-
(2011)
Sci Signal
, vol.4
-
-
Rigbolt, K.T.1
Prokhorova, T.A.2
Akimov, V.3
Henningsen, J.4
Johansen, P.T.5
Kratchmarova, I.6
Kassem, M.7
Mann, M.8
Olsen, J.V.9
Blagoev, B.10
-
46
-
-
0037924463
-
Mycobacterium tuberculosis chaperonin 10 heptamers self-associate through their biologically active loops
-
DOI 10.1128/JB.185.14.4172-4185.2003
-
Roberts MM, Coker AR, Fossati G, Mascagni P, Coates AR, Wood SP (2003) Mycobacterium tuberculosis chaperonin 10 heptamers self-associate through their biologically active loops. J Bacteriol 185: 4172-4185 (Pubitemid 36835257)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.14
, pp. 4172-4185
-
-
Roberts, M.M.1
Coker, A.R.2
Fossati, G.3
Mascagni, P.4
Coates, A.R.M.5
Wood, S.P.6
-
47
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
DOI 10.1006/jmbi.1993.1626
-
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815 (Pubitemid 24007801)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
48
-
-
73449134487
-
The stability of cytadherence proteins in Mycoplasma pneumoniae requires activity of the protein kinase PrkC
-
Schmidl SR, GronauK, HamesC, Busse J,Becher D, HeckerM,Stulke J (2010a) The stability of cytadherence proteins in Mycoplasma pneumoniae requires activity of the protein kinase PrkC. Infect Immun 78: 184-192
-
(2010)
Infect Immun
, vol.78
, pp. 184-192
-
-
Schmidl, S.R.1
Hamesc, G.2
Busse Jbecher, D.3
Heckermstulke, J.4
-
49
-
-
77953160473
-
The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: Analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases
-
Schmidl SR, Gronau K, Pietack N, Hecker M, Becher D, Stulke J (2010b) The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases. Mol Cell Proteomics 9: 1228-1242
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 1228-1242
-
-
Schmidl, S.R.1
Gronau, K.2
Pietack, N.3
Hecker, M.4
Becher, D.5
Stulke, J.6
-
50
-
-
33846014703
-
An acetylation site in the middle domain of Hsp90 regulates chaperone function
-
DOI 10.1016/j.molcel.2006.12.008, PII S1097276506008446
-
Scroggins BT, Robzyk K, Wang D, Marcu MG, Tsutsumi S, Beebe K, Cotter RJ, Felts S, Toft D, Karnitz L, Rosen N, Neckers L (2007) An acetylation site in the middle domain of Hsp90 regulates chaperone function. Mol Cell 25: 151-159 (Pubitemid 46049066)
-
(2007)
Molecular Cell
, vol.25
, Issue.1
, pp. 151-159
-
-
Scroggins, B.T.1
Robzyk, K.2
Wang, D.3
Marcu, M.G.4
Tsutsumi, S.5
Beebe, K.6
Cotter, R.J.7
Felts, S.8
Toft, D.9
Karnitz, L.10
Rosen, N.11
Neckers, L.12
-
51
-
-
4143134164
-
Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity
-
DOI 10.1016/j.str.2004.05.020, PII S0969212604002370
-
Shimamura T, Koike-Takeshita A, Yokoyama K, Masui R, Murai N, Yoshida M, Taguchi H, Iwata S (2004) Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity. Structure 12: 1471-1480 (Pubitemid 39092091)
-
(2004)
Structure
, vol.12
, Issue.8
, pp. 1471-1480
-
-
Shimamura, T.1
Koike-Takeshita, A.2
Yokoyama, K.3
Masui, R.4
Murai, N.5
Yoshida, M.6
Taguchi, H.7
Iwata, S.8
-
52
-
-
38449098746
-
Control of the phosphorylation state of the HPr protein of the phosphotransferase system in Bacillus subtilis: Implication of the protein phosphatase PrpC
-
DOI 10.1159/000103608
-
Singh KD, Halbedel S, Gorke B, Stulke J (2007) Control of the phosphorylation state of the HPr protein of the phosphotransferase system in Bacillus subtilis: implication of the protein phosphatase PrpC. J Mol Microbiol Biotechnol 13: 165-171 (Pubitemid 351359845)
-
(2007)
Journal of Molecular Microbiology and Biotechnology
, vol.13
, Issue.1-3
, pp. 165-171
-
-
Singh, K.D.1
Halbedel, S.2
Gorke, B.3
Stulke, J.4
-
53
-
-
52649125713
-
The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins
-
Soufi B, GnadF, Jensen PR, Petranovic D, Mann M, Mijakovic I, Macek B (2008) The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins. Proteomics 8: 3486-3493
-
(2008)
Proteomics
, vol.8
, pp. 3486-3493
-
-
Soufi, B.1
Gnadf Jensen, P.R.2
Petranovic, D.3
Mann, M.4
Mijakovic, I.5
MacEk, B.6
-
54
-
-
0034610814
-
The language of covalent histone modifications
-
DOI 10.1038/47412
-
Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41-45 (Pubitemid 30038513)
-
(2000)
Nature
, vol.403
, Issue.6765
, pp. 41-45
-
-
Strahl, B.D.1
Allis, C.D.2
-
55
-
-
77949786295
-
Value of using multiple proteases for large-scale mass spectrometry-based proteomics
-
Swaney DL, Wenger CD, Coon JJ (2010) Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res 9: 1323-1329
-
(2010)
J Proteome Res
, vol.9
, pp. 1323-1329
-
-
Swaney, D.L.1
Wenger, C.D.2
Coon, J.J.3
-
56
-
-
79952366305
-
RockerBox: Analysis and filtering of massive proteomics search results
-
van den Toorn HW, Munoz J, Mohammed S, Raijmakers R, Heck AJ, van Breukelen B (2011) RockerBox: analysis and filtering of massive proteomics search results. J Proteome Res 10: 1420-1424
-
(2011)
J Proteome Res
, vol.10
, pp. 1420-1424
-
-
Van Den Toorn, H.W.1
Munoz, J.2
Mohammed, S.3
Raijmakers, R.4
Heck, A.J.5
Van Breukelen, B.6
-
57
-
-
67849106825
-
Phosphorylation dynamics during early differentiation of human embryonic stem cells
-
Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J (2009) Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell 5: 214-226
-
(2009)
Cell Stem Cell
, vol.5
, pp. 214-226
-
-
Van Hoof, D.1
Munoz, J.2
Braam, S.R.3
Pinkse, M.W.4
Linding, R.5
Heck, A.J.6
Mummery, C.L.7
Krijgsveld, J.8
-
58
-
-
5644300391
-
Mycoplasma pneumoniae and its role as a human pathogen
-
Waites KB, TalkingtonDF(2004) Mycoplasma pneumoniae and its role as a human pathogen. Clin Microbiol Rev 17: 697-728, table of contents
-
(2004)
Clin Microbiol Rev
, vol.17
, pp. 697-728
-
-
Waites, K.B.1
Talkington, D.F.2
-
59
-
-
77149120797
-
Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux
-
Wang Q, Zhang Y, Yang C, Xiong H, Lin Y, Yao J, Li H, Xie L, Zhao W, Yao Y, Ning ZB, Zeng R, Xiong Y, Guan KL, Zhao S, Zhao GP (2010) Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327: 1004-1007
-
(2010)
Science
, vol.327
, pp. 1004-1007
-
-
Wang, Q.1
Zhang, Y.2
Yang, C.3
Xiong, H.4
Lin, Y.5
Yao, J.6
Li, H.7
Xie, L.8
Zhao, W.9
Yao, Y.10
Ning, Z.B.11
Zeng, R.12
Xiong, Y.13
Guan, K.L.14
Zhao, S.15
Zhao, G.P.16
-
60
-
-
79961013401
-
Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes
-
Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, Gygi SP (2011) Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol Cell Proteomics 10: M111009654
-
(2011)
Mol Cell Proteomics
, vol.10
-
-
Wu, R.1
Dephoure, N.2
Haas, W.3
Huttlin, E.L.4
Zhai, B.5
Sowa, M.E.6
Gygi, S.P.7
-
61
-
-
49349107518
-
Lysine acetylation: Codified crosstalk with other posttranslational modifications
-
Yang XJ, Seto E (2008a) Lysine acetylation: codified crosstalk with other posttranslational modifications. Mol Cell 31: 449-461
-
(2008)
Mol Cell
, vol.31
, pp. 449-461
-
-
Yang, X.J.1
Seto, E.2
-
62
-
-
39749127166
-
The Rpd3/Hda1 family of lysine deacetylases: From bacteria and yeast to mice and men
-
DOI 10.1038/nrm2346, PII NRM2346
-
Yang XJ, Seto E (2008b) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9: 206-218 (Pubitemid 351301825)
-
(2008)
Nature Reviews Molecular Cell Biology
, vol.9
, Issue.3
, pp. 206-218
-
-
Yang, X.-J.1
Seto, E.2
-
63
-
-
79961009220
-
SUMOylation-regulated protein phosphorylation, evidence from quantitative phosphoproteomics analyses
-
Yao Q, Li H, Liu BQ, Huang XY, Guo L (2011) SUMOylation-regulated protein phosphorylation, evidence from quantitative phosphoproteomics analyses. J Biol Chem 286: 27342-27349
-
(2011)
J Biol Chem
, vol.286
, pp. 27342-27349
-
-
Yao, Q.1
Li, H.2
Liu, B.Q.3
Huang, X.Y.4
Guo, L.5
-
64
-
-
56649114286
-
The diversity of lysine-acetylated proteins in Escherichia coli
-
Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008) The diversity of lysine-acetylated proteins in Escherichia coli. J Microbiol Biotechnol 18: 1529-1536
-
(2008)
J Microbiol Biotechnol
, vol.18
, pp. 1529-1536
-
-
Yu, B.J.1
Kim, J.A.2
Moon, J.H.3
Ryu, S.E.4
Pan, J.G.5
-
65
-
-
70849102021
-
Impact of genome reduction on bacterial metabolism and its regulation
-
Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Guell M, Martinez S, Bourgeois R, Kuhner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutierrez-Gallego R, Russell RB, Gavin AC, Bork P et al (2009) Impact of genome reduction on bacterial metabolism and its regulation. Science 326: 1263-1268
-
(2009)
Science
, vol.326
, pp. 1263-1268
-
-
Yus, E.1
Maier, T.2
Michalodimitrakis, K.3
Van Noort, V.4
Yamada, T.5
Chen, W.H.6
Wodke, J.A.7
Guell, M.8
Martinez, S.9
Bourgeois, R.10
Kuhner, S.11
Raineri, E.12
Letunic, I.13
Kalinina, O.V.14
Rode, M.15
Herrmann, R.16
Gutierrez-Gallego, R.17
Russell, R.B.18
Gavin, A.C.19
Bork, P.20
more..
-
66
-
-
61649089277
-
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli
-
Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009a) Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics 8: 215-225
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 215-225
-
-
Zhang, J.1
Sprung, R.2
Pei, J.3
Tan, X.4
Kim, S.5
Zhu, H.6
Liu, C.F.7
Grishin, N.V.8
Zhao, Y.9
-
67
-
-
59649126261
-
Deacetylation of cortactin by SIRT1 promotes cell migration
-
Zhang Y, Zhang M, Dong H, Yong S, Li X, Olashaw N, Kruk PA, Cheng JQ, Bai W, Chen J, Nicosia SV, Zhang X (2009b) Deacetylation of cortactin by SIRT1 promotes cell migration. Oncogene 28: 445-460
-
(2009)
Oncogene
, vol.28
, pp. 445-460
-
-
Zhang, Y.1
Zhang, M.2
Dong, H.3
Yong, S.4
Li, X.5
Olashaw, N.6
Kruk, P.A.7
Cheng, J.Q.8
Bai, W.9
Chen, J.10
Nicosia, S.V.11
Zhang, X.12
-
68
-
-
77149148756
-
Regulation of cellular metabolism by protein lysine acetylation
-
Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q et al (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327: 1000-1004
-
(2010)
Science
, vol.327
, pp. 1000-1004
-
-
Zhao, S.1
Xu, W.2
Jiang, W.3
Yu, W.4
Lin, Y.5
Zhang, T.6
Yao, J.7
Zhou, L.8
Zeng, Y.9
Li, H.10
Li, Y.11
Shi, J.12
An, W.13
Hancock, S.M.14
He, F.15
Qin, L.16
Chin, J.17
Yang, P.18
Chen, X.19
Lei, Q.20
more..
-
69
-
-
79958838890
-
Eukaryotic-like Ser/Thr protein kinases SpkC/F/K are involved in phosphorylation of GroES in the Cyanobacterium synechocystis
-
Zorina A, Stepanchenko N, Novikova GV, Sinetova M, Panichkin VB, Moshkov IE, Zinchenko VV, Shestakov SV, Suzuki I, Murata N, Los DA (2011) Eukaryotic-like Ser/Thr protein kinases SpkC/F/K are involved in phosphorylation of GroES in the Cyanobacterium synechocystis. DNA Res 18: 137-151
-
(2011)
DNA Res
, vol.18
, pp. 137-151
-
-
Zorina, A.1
Stepanchenko, N.2
Novikova, G.V.3
Sinetova, M.4
Panichkin, V.B.5
Moshkov, I.E.6
Zinchenko, V.V.7
Shestakov, S.V.8
Suzuki, I.9
Murata, N.10
Los, D.A.11
|