-
1
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
-
2
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
3
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin,A.C., Aloy,P., Grandi,P., Krause,R., Boesche,M., Marzioch,M., Rau,C., Jensen,L.J., Bastuck,S., Dumpelfeld,B. et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature., 440, 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dumpelfeld, B.10
-
4
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
-
5
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bosche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
-
6
-
-
0037245913
-
Bind: The biomolecular interaction network database
-
Bader,G.D., Betel,D. and Hogue,C.W. (2003) Bind: The biomolecular interaction network database. Nucleic Acids Res., 31, 248-250.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
7
-
-
0347755535
-
The Database of Interacting Proteins: 2004 update
-
Salwinski,L., Miller,C.S., Smith,A.J., Pettit,F.K., Bowie,J.U. and Eisenberg,D. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
8
-
-
0037832188
-
Computational methods of analysis of protein-protein interactions
-
Salwinski,L. and Eisenberg,D. (2003) Computational methods of analysis of protein-protein interactions. Curr. Opin. Struct. Biol., 13, 377-382.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 377-382
-
-
Salwinski, L.1
Eisenberg, D.2
-
9
-
-
0142052944
-
A bayesian networks approach for predicting protein-protein interactions from genomic data
-
Jansen,R., Yu,H., Greenbaum,D., Kluger,Y., Krogan,N.J., Chung,S., Emili,A., Snyder,M., Greenblatt,J.F. and Gerstein,M. (2003) A bayesian networks approach for predicting protein-protein interactions from genomic data. Science, 302, 449-453.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.J.5
Chung, S.6
Emili, A.7
Snyder, M.8
Greenblatt, J.F.9
Gerstein, M.10
-
10
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
Lee,I., Date,S.V., Adai,A.T. and Marcotte,E.M. (2004) A probabilistic functional network of yeast genes. Science, 306, 1555-1558.
-
(2004)
Science
, vol.306
, pp. 1555-1558
-
-
Lee, I.1
Date, S.V.2
Adai, A.T.3
Marcotte, E.M.4
-
11
-
-
22244447463
-
Assessing the limits of genomic data integration for predicting protein networks
-
Lu,L.J., Xia,Y., Paccanaro,A., Yu,H. and Gerstein,M. (2005) Assessing the limits of genomic data integration for predicting protein networks. Genome Res., 15, 945-953.
-
(2005)
Genome Res.
, vol.15
, pp. 945-953
-
-
Lu, L.J.1
Xia, Y.2
Paccanaro, A.3
Yu, H.4
Gerstein, M.5
-
12
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy,P. and Russell,R.B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
13
-
-
0037110589
-
MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading
-
Lu,L., Lu,H. and Skolnick,J. (2002) MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins, 49, 330-364.
-
(2002)
Proteins
, vol.49
, pp. 330-364
-
-
Lu, L.1
Lu, H.2
Skolnick, J.3
-
14
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
Aloy,P., Bottcher,B., Ceulemans,H., Leutwein,C., Mellwig,C., Fischer,S., Garin,A.C., Bork,P., Superti-Furga,G., Serrano,L. et al. (2004) Structure-based assembly of protein complexes in yeast. Science, 303, 2026-2029.
-
(2004)
Science
, vol.303
, pp. 2026-2029
-
-
Aloy, P.1
Bottcher, B.2
Ceulemans, H.3
Leutwein, C.4
Mellwig, C.5
Fischer, S.6
Garin, A.C.7
Bork, P.8
Superti-Furga, G.9
Serrano, L.10
-
15
-
-
16344381315
-
Statistical analysis of domains in interacting protein pairs
-
Nye,T.M., Berzuini,C., Gilks,W.R., Babu,M.M. and Teichmann,S.A. (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics, 21, 993-1001.
-
(2005)
Bioinformatics
, vol.21
, pp. 993-1001
-
-
Nye, T.M.1
Berzuini, C.2
Gilks, W.R.3
Babu, M.M.4
Teichmann, S.A.5
-
16
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
Bader,G.D. and Hogue,C.W. (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
17
-
-
0142059836
-
Protein complexes and functional modules in molecular networks
-
Spirin,V. and Mirny,L.A. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl Acad. Sci. USA, 100, 12123-12128.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 12123-12128
-
-
Spirin, V.1
Mirny, L.A.2
-
18
-
-
6344260294
-
The power of two: Protein dimerization in biology
-
Marianayagam,N.J., Sunde,M. and Matthews,J.M. (2004) The power of two: protein dimerization in biology. Trends Biochem Sci., 29, 618-625.
-
(2004)
Trends Biochem Sci.
, vol.29
, pp. 618-625
-
-
Marianayagam, N.J.1
Sunde, M.2
Matthews, J.M.3
-
19
-
-
18744382508
-
PIBASE: A comprehensive database of structurally defined protein interfaces
-
Davis,F.P. and Sali,A. (2005) PIBASE: A comprehensive database of structurally defined protein interfaces. Bioinformatics, 21, 1901-1907.
-
(2005)
Bioinformatics
, vol.21
, pp. 1901-1907
-
-
Davis, F.P.1
Sali, A.2
-
20
-
-
0033954256
-
The Protein Data Bank
-
Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, 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
-
21
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
22
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo,F., Sanchez,R. and Sali,A. (2002) Statistical potentials for fold assessment. Protein Sci., 11, 430-448.
-
(2002)
Protein Sci.
, vol.11
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
23
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami,S., Huh,W.K., Bower,K., Howson,R.W., Belle,A., Dephoure,N., O'Shea,E.K. and Weissman,J.S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
24
-
-
0036087548
-
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the gene ontology (GO)
-
Dwight,S.S., Harris,M.A., Dolinski,K., Ball,C.A., Binkley,G., Christie,K.R., Fisk,D.G., Issel-Tarver,L., Schroeder,M., Sherlock,G. et al. (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the gene ontology (GO). Nucleic Acids Res., 30, 69-72.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 69-72
-
-
Dwight, S.S.1
Harris, M.A.2
Dolinski, K.3
Ball, C.A.4
Binkley, G.5
Christie, K.R.6
Fisk, D.G.7
Issel-Tarver, L.8
Schroeder, M.9
Sherlock, G.10
-
25
-
-
0345438685
-
ROC graphs: Notes and practical considerations for data mining researchers
-
HP Labs, Palo Alto, CA, USA
-
Fawcett,T. (2003) ROC graphs: Notes and practical considerations for data mining researchers. Technical Report HPL-2003-4, HP Labs, Palo Alto, CA, USA.
-
(2003)
Technical Report HPL-2003-4
-
-
Fawcett, T.1
-
26
-
-
33644874394
-
MODBASE: A database of annotated comparative protein structure models and associated resources
-
Pieper,U., Eswar,N., Davis,F.P., Braberg,H., Madhusudhan,M.S., Rossi,A., Marti-Renom,M., Karchin,R., Webb,B.M., Eranian,D. et al. (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res., 34, D291-D295.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Pieper, U.1
Eswar, N.2
Davis, F.P.3
Braberg, H.4
Madhusudhan, M.S.5
Rossi, A.6
Marti-Renom, M.7
Karchin, R.8
Webb, B.M.9
Eranian, D.10
-
27
-
-
0043123167
-
Tools for comparative protein structure modeling and analysis
-
Eswar,N., John,B., Mirkovic,N., Fiser,A., Ilyin,V.A., Pieper,U., Stuart,A.C., Marti-Renom,M.A., Madhusudhan,M.S., Yerkovich,B. et al. (2003) Tools for comparative protein structure modeling and analysis. Nucleic Acids Res., 31, 3375-3380.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3375-3380
-
-
Eswar, N.1
John, B.2
Mirkovic, N.3
Fiser, A.4
Ilyin, V.A.5
Pieper, U.6
Stuart, A.C.7
Marti-Renom, M.A.8
Madhusudhan, M.S.9
Yerkovich, B.10
-
28
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
29
-
-
0348129526
-
The ASTRAL Compendium in 2004
-
Chandonia,J.M., Hon,G., Walker,N.S., Conte,L.L., Koehl,P., Levitt,M. and Brenner,S.E. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Chandonia, J.M.1
Hon, G.2
Walker, N.S.3
Conte, L.L.4
Koehl, P.5
Levitt, M.6
Brenner, S.E.7
-
30
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick,K. and Thornton,J.M. (1998) PQS: A protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
31
-
-
0038817799
-
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome
-
Lu,L., Arakaki,A.K., Lu,H. and Skolnick,J. (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome. Genome Res., 13, 1146-1154.
-
(2003)
Genome Res.
, vol.13
, pp. 1146-1154
-
-
Lu, L.1
Arakaki, A.K.2
Lu, H.3
Skolnick, J.4
-
32
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3003.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2994-3003
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
33
-
-
0344447084
-
Potent enzyme inhibitors derived from dromedary heavy-chain antibodies
-
Lauwereys,M., Ghahroudi,M.A., Desmyter,A., Kinne,J., Holzer,W., Genst,E.D., Wyns,L. and Muyldermans,S. (1998) Potent enzyme inhibitors derived from dromedary heavy-chain antibodies. EMBO J., 17, 3512-3520.
-
(1998)
EMBO J.
, vol.17
, pp. 3512-3520
-
-
Lauwereys, M.1
Ghahroudi, M.A.2
Desmyter, A.3
Kinne, J.4
Holzer, W.5
Genst, E.D.6
Wyns, L.7
Muyldermans, S.8
-
34
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
35
-
-
25844494381
-
Comparative Protein Structure Modeling
-
In Walker,J.M. (ed.), Humana Press Inc., Totowa, NJ
-
Madhusudhan,M.S., Marti-Renom,M.A., Eswar,N., John,B., Pieper,U., Karchin,R., Shen,M.Y. and Sali,A. (2005) Comparative Protein Structure Modeling. In Walker,J.M. (ed.), The Proteomics Protocols Handbook. Humana Press Inc., Totowa, NJ, pp. 831-860.
-
(2005)
The Proteomics Protocols Handbook
, pp. 831-860
-
-
Madhusudhan, M.S.1
Marti-Renom, M.A.2
Eswar, N.3
John, B.4
Pieper, U.5
Karchin, R.6
Shen, M.Y.7
Sali, A.8
-
36
-
-
0035861532
-
Systematic genetic analysis with ordered arrays of yeast deletion mutants
-
Tong,A.H., Evangelista,M., Parsons,A.B., Xu,H., Bader,G.D., Page,N., Robinson,M., Raghibizadeh,S., Hogue,C.W., Bussey,H. et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science, 294, 2364-2368.
-
(2001)
Science
, vol.294
, pp. 2364-2368
-
-
Tong, A.H.1
Evangelista, M.2
Parsons, A.B.3
Xu, H.4
Bader, G.D.5
Page, N.6
Robinson, M.7
Raghibizadeh, S.8
Hogue, C.W.9
Bussey, H.10
-
37
-
-
25444531429
-
Computational verification of protein-protein interactions by orthologous co-expression
-
Tirosh,I. and Barkai,N. (2005) Computational verification of protein-protein interactions by orthologous co-expression. BMC Bioinformatics, 6, 40.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 40
-
-
Tirosh, I.1
Barkai, N.2
-
38
-
-
3042569597
-
Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs
-
Yu,H., Luscombe,N.M., Lu,H.X., Zhu,X., Xia,Y., Han,J.D., Bertin,N., Chung,S., Vidal,M. and Gerstein,M. (2004) Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs. Genome Res., 14, 1107-1118.
-
(2004)
Genome Res.
, vol.14
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.M.2
Lu, H.X.3
Zhu, X.4
Xia, Y.5
Han, J.D.6
Bertin, N.7
Chung, S.8
Vidal, M.9
Gerstein, M.10
-
39
-
-
15044350197
-
The evolution of domain arrangements in proteins and interaction networks
-
Bornberg-Bauer,E., Beaussart,F., Kummerfeld,S.K., Teichmann,S.A. and Weiner,J.,III (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol. Life Sci., 62, 435-445.
-
(2005)
Cell Mol. Life Sci.
, vol.62
, pp. 435-445
-
-
Bornberg-Bauer, E.1
Beaussart, F.2
Kummerfeld, S.K.3
Teichmann, S.A.4
Weiner III, J.5
-
40
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han,J.D., Bertin,N., Hao,T., Goldberg,D.S., Berriz,G.F., Zhang,L.V., Dupuy,D., Walhout,A.J., Cusick,M.E., Roth,F.P. et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.8
Cusick, M.E.9
Roth, F.P.10
-
41
-
-
25844459522
-
Combining electron microscopy and comparative protein structure modeling
-
Topf,M. and Sali,A. (2005) Combining electron microscopy and comparative protein structure modeling. Curr. Opin. Struct. Biol., 15, 578-585.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 578-585
-
-
Topf, M.1
Sali, A.2
-
42
-
-
14844311200
-
Fitting of high-resolution structures into electron microscopy reconstruction images
-
Fabiola,F. and Chapman,M.S. (2005) Fitting of high-resolution structures into electron microscopy reconstruction images. Structure, 13, 389-400.
-
(2005)
Structure
, vol.13
, pp. 389-400
-
-
Fabiola, F.1
Chapman, M.S.2
-
43
-
-
0037435031
-
From words to literature in structural proteomics
-
Sali,A., Glaeser,R., Earnest,T. and Baumeister,W. (2003) From words to literature in structural proteomics. Nature, 422, 216-225.
-
(2003)
Nature
, vol.422
, pp. 216-225
-
-
Sali, A.1
Glaeser, R.2
Earnest, T.3
Baumeister, W.4
-
44
-
-
5044235050
-
Ten thousand interactions for the molecular biologist
-
Aloy,P. and Russell,R.B. (2004) Ten thousand interactions for the molecular biologist. Nat. Biotechnol., 22, 1317-1321.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1317-1321
-
-
Aloy, P.1
Russell, R.B.2
|