-
1
-
-
19344362896
-
Towards cellular systems in 4D
-
Bork P., and Serrano L. Towards cellular systems in 4D. Cell 121 (2005) 507-509
-
(2005)
Cell
, vol.121
, pp. 507-509
-
-
Bork, P.1
Serrano, L.2
-
2
-
-
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. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 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
-
3
-
-
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. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 (2002) 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
-
4
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
This study describes a genome-wide screen for complexes in budding yeast, using affinity purification and mass spectrometry. It compiled, in a systematic way, the largest collection of experimentally determined eukaryotic cellular machines to date, revealing the modularity of S. cerevisiae cellular network.
-
Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dumpelfeld B., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 (2006) 631-636. This study describes a genome-wide screen for complexes in budding yeast, using affinity purification and mass spectrometry. It compiled, in a systematic way, the largest collection of experimentally determined eukaryotic cellular machines to date, revealing the modularity of S. cerevisiae cellular network.
-
(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
-
5
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual J.F., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., Berriz G.F., Gibbons F.D., Dreze M., Ayivi-Guedehoussou N., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (2005) 1173-1178
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
Li, N.6
Berriz, G.F.7
Gibbons, F.D.8
Dreze, M.9
Ayivi-Guedehoussou, N.10
-
6
-
-
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. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403 (2000) 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
-
7
-
-
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. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98 (2001) 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
-
8
-
-
25144498379
-
A human protein-protein interaction network: a resource for annotating the proteome
-
Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F.H., Goehler H., Stroedicke M., Zenkner M., Schoenherr A., Koeppen S., et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122 (2005) 957-968
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
-
9
-
-
33749535603
-
Co-evolution of transcriptional and post-translational cell-cycle regulation
-
Jensen L.J., Jensen T.S., de Lichtenberg U., Brunak S., and Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443 (2006) 594-597
-
(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
-
10
-
-
33947419351
-
An evaluation of human protein-protein interaction data in the public domain
-
Mathivanan S., Periaswamy B., Gandhi T., Kandasamy K., Suresh S., Mohmood R., Ramachandra Y., and Pandey A. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 7 suppl 5 (2006) S19
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 5
-
-
Mathivanan, S.1
Periaswamy, B.2
Gandhi, T.3
Kandasamy, K.4
Suresh, S.5
Mohmood, R.6
Ramachandra, Y.7
Pandey, A.8
-
11
-
-
33644550021
-
Structural systems biology: modelling protein interactions
-
Aloy P., and Russell R.B. Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 3 (2006) 188-197
-
(2006)
Nat Rev Mol Cell Biol
, vol.3
, pp. 188-197
-
-
Aloy, P.1
Russell, R.B.2
-
12
-
-
13844293072
-
Recognizing and defining true Ras binding domains II: In silico prediction based on homology modelling and energy calculations
-
Kiel C., Wohlgemuth S., Rousseau F., Schymkowitz J., Ferkinghoff-Borg J., Wittinghofer F., and Serrano L. Recognizing and defining true Ras binding domains II: In silico prediction based on homology modelling and energy calculations. J Mol Biol 348 (2005) 759-775
-
(2005)
J Mol Biol
, vol.348
, pp. 759-775
-
-
Kiel, C.1
Wohlgemuth, S.2
Rousseau, F.3
Schymkowitz, J.4
Ferkinghoff-Borg, J.5
Wittinghofer, F.6
Serrano, L.7
-
14
-
-
34347375373
-
Affinity can have many faces: thermodynamic and kinetic properties of Ras-effector complex formation
-
Kiel C., and Serrano L. Affinity can have many faces: thermodynamic and kinetic properties of Ras-effector complex formation. Curr Chem Biol 1 (2007) 215-225
-
(2007)
Curr Chem Biol
, vol.1
, pp. 215-225
-
-
Kiel, C.1
Serrano, L.2
-
15
-
-
14844328879
-
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks
-
Ander M., Beltrao P., Di Ventura B., Ferkinghoff-Borg J., Foglierini M., Kaplan A., Lemerle C., Tomas-Oliveira I., and Serrano L. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst Biol 1 (2004) 129-138
-
(2004)
Syst Biol
, vol.1
, pp. 129-138
-
-
Ander, M.1
Beltrao, P.2
Di Ventura, B.3
Ferkinghoff-Borg, J.4
Foglierini, M.5
Kaplan, A.6
Lemerle, C.7
Tomas-Oliveira, I.8
Serrano, L.9
-
16
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
-
Guerois R., Nielsen J.E., and Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320 (2002) 369-387
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
17
-
-
23144436398
-
The FoldX web server: an online force field
-
Schymkowitz J., Borg J., Stricher F., Nys R., Rousseau F., and Serrano L. The FoldX web server: an online force field. Nucleic Acids Res 33 (2005) W382-W388
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
18
-
-
22544450150
-
Prediction of water and metal binding sites and their affinities by using the Fold-X force field
-
Schymkowitz J.W.H., Rousseau F., Martins I.C., Ferkinghoff-Borg J., Stricher F., and Serrano L. Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci USA 102 (2005) 10147-10152
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10147-10152
-
-
Schymkowitz, J.W.H.1
Rousseau, F.2
Martins, I.C.3
Ferkinghoff-Borg, J.4
Stricher, F.5
Serrano, L.6
-
19
-
-
3242797452
-
A detailed thermodynamic analysis of Ras/effector complex interfaces
-
Kiel C., Serrano L., and Herrmann C. A detailed thermodynamic analysis of Ras/effector complex interfaces. J Mol Biol 340 (2004) 1039-1058
-
(2004)
J Mol Biol
, vol.340
, pp. 1039-1058
-
-
Kiel, C.1
Serrano, L.2
Herrmann, C.3
-
20
-
-
17144384463
-
Recognizing and defining true Ras binding domains I: Biochemical analysis
-
Wohlgemuth S., Kiel C., Kraemer A., Serrano L., Wittinghofer F., and Herrmann C. Recognizing and defining true Ras binding domains I: Biochemical analysis. J Mol Biol 348 (2005) 741-758
-
(2005)
J Mol Biol
, vol.348
, pp. 741-758
-
-
Wohlgemuth, S.1
Kiel, C.2
Kraemer, A.3
Serrano, L.4
Wittinghofer, F.5
Herrmann, C.6
-
21
-
-
29144518532
-
The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes
-
Kiel C., and Serrano L. The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J Mol Biol 355 (2006) 821-844
-
(2006)
J Mol Biol
, vol.355
, pp. 821-844
-
-
Kiel, C.1
Serrano, L.2
-
22
-
-
33746067899
-
Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6
-
Kempkens O., Médina E., Fernandez-Ballester G., Özüyaman S., Le Bivic A., Serrano L., and Knust E. Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur J Cell Biol 8 (2006) 753-767
-
(2006)
Eur J Cell Biol
, vol.8
, pp. 753-767
-
-
Kempkens, O.1
Médina, E.2
Fernandez-Ballester, G.3
Özüyaman, S.4
Le Bivic, A.5
Serrano, L.6
Knust, E.7
-
23
-
-
33645510752
-
New approaches to high-throughput structure characterization of SH3 complexes: the example of myosin-3 and myosin-5 SH3 domains from S. cerevisiae
-
Musi V., Birdsall B., Fernandez-Ballester G., Guerrini R., Salvatori S., Serrano L., and Pastore A. New approaches to high-throughput structure characterization of SH3 complexes: the example of myosin-3 and myosin-5 SH3 domains from S. cerevisiae. Protein Sci 4 (2006) 795-807
-
(2006)
Protein Sci
, vol.4
, pp. 795-807
-
-
Musi, V.1
Birdsall, B.2
Fernandez-Ballester, G.3
Guerrini, R.4
Salvatori, S.5
Serrano, L.6
Pastore, A.7
-
24
-
-
33745056174
-
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor
-
By using the automatic design algorithm FOLD-X, DR5-selective TRAIL variants have been generated. These variants do not induce apoptosis in DR4-responsive cell lines, but show a large increase in biological activity in DR5-responsive cancer cell lines. This study shows that the specificity of protein-protein interactions can be successfully modified using computational protein design without having high-quality structural data available for all relevant interactions. Moreover, it demonstrates that changing the specificity of protein-protein interactions using computational design could be a valuable approach for designing novel therapeutics.
-
Van der Sloot A.M., Tur V., Szegezdi E., Mullally M.M., Cool R.H., Samali A., Serrano L., and Quax W.J. Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci USA 103 (2006) 8634-8639. By using the automatic design algorithm FOLD-X, DR5-selective TRAIL variants have been generated. These variants do not induce apoptosis in DR4-responsive cell lines, but show a large increase in biological activity in DR5-responsive cancer cell lines. This study shows that the specificity of protein-protein interactions can be successfully modified using computational protein design without having high-quality structural data available for all relevant interactions. Moreover, it demonstrates that changing the specificity of protein-protein interactions using computational design could be a valuable approach for designing novel therapeutics.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 8634-8639
-
-
Van der Sloot, A.M.1
Tur, V.2
Szegezdi, E.3
Mullally, M.M.4
Cool, R.H.5
Samali, A.6
Serrano, L.7
Quax, W.J.8
-
25
-
-
1842577654
-
Computational redesign of protein-protein interaction specificity
-
Kortemme T., Joachimiak L.A., Bullock A.N., Schuler A.D., Stoddard B.L., and Baker D. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 11 (2004) 371-379
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 371-379
-
-
Kortemme, T.1
Joachimiak, L.A.2
Bullock, A.N.3
Schuler, A.D.4
Stoddard, B.L.5
Baker, D.6
-
26
-
-
33745927413
-
Computational design of a new hydrogen bond network at a protein-protein interface
-
Joachimiak L.A., Kortemme T., Stoddard B.L., and Baker D. Computational design of a new hydrogen bond network at a protein-protein interface. J Mol Biol 361 (2006) 195-208
-
(2006)
J Mol Biol
, vol.361
, pp. 195-208
-
-
Joachimiak, L.A.1
Kortemme, T.2
Stoddard, B.L.3
Baker, D.4
-
27
-
-
33646173276
-
Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion
-
Song G., Lazar G.A., Kortemme T., Shimaoka M., Desjarlais J.R., Baker D., and Springer T.A. Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. J Biol Chem 281 (2006) 5042-5049
-
(2006)
J Biol Chem
, vol.281
, pp. 5042-5049
-
-
Song, G.1
Lazar, G.A.2
Kortemme, T.3
Shimaoka, M.4
Desjarlais, J.R.5
Baker, D.6
Springer, T.A.7
-
28
-
-
0034039797
-
Electrostatic aspects of protein-protein interactions
-
Sheinerman F.B., Norel R., and Honig B. Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol 10 (2000) 153-159
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 153-159
-
-
Sheinerman, F.B.1
Norel, R.2
Honig, B.3
-
29
-
-
0033923367
-
Rational design of faster associating and tighter binding protein complexes
-
PARE is a protein design strategy to enhance the rate constant of association by increasing the electrostatic attraction between a protein pair. A very high correlation is found between experimentally determined association rate constants for mutants and calculated changes in association rate constants relative to the wild-type complex. Using this design strategy and maintaining the dissociation rate constant, the affinity between TEM1 and its protein inhibitor, BLIP, could be enhanced 250-fold.
-
Selzer T., Albeck S., and Schreiber G. Rational design of faster associating and tighter binding protein complexes. Nat Struct Biol 7 (2000) 537-541. PARE is a protein design strategy to enhance the rate constant of association by increasing the electrostatic attraction between a protein pair. A very high correlation is found between experimentally determined association rate constants for mutants and calculated changes in association rate constants relative to the wild-type complex. Using this design strategy and maintaining the dissociation rate constant, the affinity between TEM1 and its protein inhibitor, BLIP, could be enhanced 250-fold.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 537-541
-
-
Selzer, T.1
Albeck, S.2
Schreiber, G.3
-
30
-
-
3042594710
-
Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex
-
Kiel C., Selzer T., Shaul Y., Schreiber G., and Herrmann C. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc Natl Acad Sci USA 101 (2004) 9223-9228
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9223-9228
-
-
Kiel, C.1
Selzer, T.2
Shaul, Y.3
Schreiber, G.4
Herrmann, C.5
-
31
-
-
2342426308
-
Optimizing the binding affinity of a carrier protein: a case study on the interaction between soluble ifnar2 and interferon beta
-
Peleg-Shulman T., Roisman L.C., Zupkovitz G., and Schreiber G. Optimizing the binding affinity of a carrier protein: a case study on the interaction between soluble ifnar2 and interferon beta. J Biol Chem 279 (2004) 18046-18053
-
(2004)
J Biol Chem
, vol.279
, pp. 18046-18053
-
-
Peleg-Shulman, T.1
Roisman, L.C.2
Zupkovitz, G.3
Schreiber, G.4
-
32
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi A.-L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 5 (2004) 101-113
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.-L.1
Oltvai, Z.N.2
-
33
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H., Tombor B., Albert R., Oltvai Z.N., and Barabasi A.L. The large-scale organization of metabolic networks. Nature 407 (2000) 651-654
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
35
-
-
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. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430 (2004) 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
-
36
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
This study shows that it is possible to discriminate between different node types, in metabolic networks, by analyzing the edges occurring within and/or between modules. The ability to use topological information to identify modules and different node types underscores the usefulness of the network formalism for the study of cellular pathways.
-
Guimera R., and Nunes Amaral L.A. Functional cartography of complex metabolic networks. Nature 433 (2005) 895-900. This study shows that it is possible to discriminate between different node types, in metabolic networks, by analyzing the edges occurring within and/or between modules. The ability to use topological information to identify modules and different node types underscores the usefulness of the network formalism for the study of cellular pathways.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimera, R.1
Nunes Amaral, L.A.2
-
37
-
-
33845969217
-
Classes of complex networks defined by role-to-role connectivity profiles
-
Guimerà R., Sales-Pardo M., and Nunes Amaral L.A. Classes of complex networks defined by role-to-role connectivity profiles. Nature Physics 3 (2007) 63-69
-
(2007)
Nature Physics
, vol.3
, pp. 63-69
-
-
Guimerà, R.1
Sales-Pardo, M.2
Nunes Amaral, L.A.3
-
38
-
-
13844264506
-
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
-
Finn R.D., Marshall M., and Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21 (2005) 410-412
-
(2005)
Bioinformatics
, vol.21
, pp. 410-412
-
-
Finn, R.D.1
Marshall, M.2
Bateman, A.3
-
39
-
-
13444257903
-
3did: interacting protein domains of known three-dimensional structure
-
Stein A., Russell R.B., and Aloy P. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res 33 (2005) D413-D417
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Stein, A.1
Russell, R.B.2
Aloy, P.3
-
41
-
-
23144463510
-
PRISM: protein interactions by structural matching
-
Ogmen U., Keskin O., Aytuna A.S., Nussinov R., and Gursoy A. PRISM: protein interactions by structural matching. Nucleic Acids Res 33 (2005) W331-W336
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Ogmen, U.1
Keskin, O.2
Aytuna, A.S.3
Nussinov, R.4
Gursoy, A.5
-
42
-
-
33846052595
-
SNAPPI-DB: a database and API of structures, interfaces and alignments for protein-protein interactions
-
Jefferson E.R., Walsh T.P., Roberts T.J., and Barton G.J. SNAPPI-DB: a database and API of structures, interfaces and alignments for protein-protein interactions. Nucleic Acids Res 35 (2007) D580-D589
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Jefferson, E.R.1
Walsh, T.P.2
Roberts, T.J.3
Barton, G.J.4
-
43
-
-
18744382508
-
PIBASE: a comprehensive database of structurally defined protein interfaces
-
Davis F.P., and Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21 (2005) 1901-1907
-
(2005)
Bioinformatics
, vol.21
, pp. 1901-1907
-
-
Davis, F.P.1
Sali, A.2
-
44
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
This is the first large-scale curation effort using structural information on binding interfaces. Using the iPfam database, the authors determined the most likely binding interface for all S. cerevisiae protein-protein interactions. This information was used to show that protein essentiality/lethality, protein sequence conservation and co-expression of binding partners are dependent on the number of binding interfaces.
-
Kim P.M., Lu L.J., Xia Y., and Gerstein M.B. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314 (2006) 1938-1941. This is the first large-scale curation effort using structural information on binding interfaces. Using the iPfam database, the authors determined the most likely binding interface for all S. cerevisiae protein-protein interactions. This information was used to show that protein essentiality/lethality, protein sequence conservation and co-expression of binding partners are dependent on the number of binding interfaces.
-
(2006)
Science
, vol.314
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
45
-
-
33847249901
-
Specificity and evolvability in eukaryotic protein interaction networks
-
Beltrao P., and Serrano L. Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol 3 (2007) e25
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Beltrao, P.1
Serrano, L.2
-
47
-
-
33748976313
-
Understanding the cell in terms of structure and function: insights from structural genomics
-
Rigden D.J. Understanding the cell in terms of structure and function: insights from structural genomics. Curr Opin Biotechnol 5 (2006) 457-464
-
(2006)
Curr Opin Biotechnol
, vol.5
, pp. 457-464
-
-
Rigden, D.J.1
-
48
-
-
33744779891
-
Sequence comparison and protein structure prediction
-
Dunbrack Jr. R.L. Sequence comparison and protein structure prediction. Curr Opin Struct Biol 16 (2006) 374-384
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 374-384
-
-
Dunbrack Jr., R.L.1
-
49
-
-
33846925964
-
The molecular architecture of protein-protein binding sites
-
Reichmann D., Rahat O., Cohen M., Neuvirth H., and Schreiber G. The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol 17 (2007) 67-76
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 67-76
-
-
Reichmann, D.1
Rahat, O.2
Cohen, M.3
Neuvirth, H.4
Schreiber, G.5
-
50
-
-
14744267674
-
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications
-
Kim J.S., DeGiovanni A., Jancarik J., Adams P.D., Yokota H., Kim R., and Kim S.H. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc Natl Acad Sci USA 102 (2005) 3248-3253
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 3248-3253
-
-
Kim, J.S.1
DeGiovanni, A.2
Jancarik, J.3
Adams, P.D.4
Yokota, H.5
Kim, R.6
Kim, S.H.7
-
51
-
-
33846847701
-
Rap1: a key regulator in cell-cell junction formation
-
Kooistra M.R.H., Dube N., and Bos J.L. Rap1: a key regulator in cell-cell junction formation. J Cell Sci 120 (2007) 17-22
-
(2007)
J Cell Sci
, vol.120
, pp. 17-22
-
-
Kooistra, M.R.H.1
Dube, N.2
Bos, J.L.3
-
52
-
-
22244447463
-
Assessing the limits of genomic data integration for predicting protein networks
-
Lu L.J., Xia Y., Paccanaro A., Yu H., and Gerstein M. Assessing the limits of genomic data integration for predicting protein networks. Genome Res 15 (2005) 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
-
53
-
-
7944229979
-
Stable kinetochore-microtubule attachment constrains centromere positioning in metaphase
-
Pearson C.G., Yeh E., Gardner M., Odde D., Salmon E.D., and Bloom K. Stable kinetochore-microtubule attachment constrains centromere positioning in metaphase. Curr Biol 14 (2004) 1962-1967
-
(2004)
Curr Biol
, vol.14
, pp. 1962-1967
-
-
Pearson, C.G.1
Yeh, E.2
Gardner, M.3
Odde, D.4
Salmon, E.D.5
Bloom, K.6
-
54
-
-
23044453524
-
Tension-dependent regulation of microtubule dynamics at kinetochores can explain metaphase congression in yeast
-
Gardner M.K., Pearson C.G., Sprague B.L., Zarzar T.R., Bloom K., Salmon E.D., and Odde D.J. Tension-dependent regulation of microtubule dynamics at kinetochores can explain metaphase congression in yeast. Mol Biol Cell 16 (2005) 3764-3775
-
(2005)
Mol Biol Cell
, vol.16
, pp. 3764-3775
-
-
Gardner, M.K.1
Pearson, C.G.2
Sprague, B.L.3
Zarzar, T.R.4
Bloom, K.5
Salmon, E.D.6
Odde, D.J.7
-
55
-
-
33746549172
-
Measuring nanometer scale gradients in spindle microtubule dynamics using model convolution microscopy
-
Pearson C.G., Gardner M.K., Paliulis L.V., Salmon E.D., Odde D.J., and Bloom K. Measuring nanometer scale gradients in spindle microtubule dynamics using model convolution microscopy. Mol Biol Cell 17 (2006) 4069-4079
-
(2006)
Mol Biol Cell
, vol.17
, pp. 4069-4079
-
-
Pearson, C.G.1
Gardner, M.K.2
Paliulis, L.V.3
Salmon, E.D.4
Odde, D.J.5
Bloom, K.6
-
56
-
-
0035865322
-
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
-
Sachidanandam R., Weissman D., Schmidt S., Kakol J., Stein L., Marth G., Sherry S., Mullikin J., Mortimore B., Willey D., et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 (2001) 928-933
-
(2001)
Nature
, vol.409
, pp. 928-933
-
-
Sachidanandam, R.1
Weissman, D.2
Schmidt, S.3
Kakol, J.4
Stein, L.5
Marth, G.6
Sherry, S.7
Mullikin, J.8
Mortimore, B.9
Willey, D.10
-
57
-
-
0037250403
-
The SNP Consortium website: past, present and future
-
Thorisson G.A., and Stein L.D. The SNP Consortium website: past, present and future. Nucleic Acids Res 31 (2003) 124-127
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 124-127
-
-
Thorisson, G.A.1
Stein, L.D.2
-
58
-
-
0036713510
-
Human non-synonymous SNPs: server and survey
-
Ramensky V., Bork P., and Sunyaey S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30 (2002) 3894-3900
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3894-3900
-
-
Ramensky, V.1
Bork, P.2
Sunyaey, S.3
-
59
-
-
13444270842
-
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
-
Reumers J., Schymkowitz J., Ferkinghoff-Borg J., Stricher F., Serrano L., and Rousseau F. SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res 33 (2005) D527-D532
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Reumers, J.1
Schymkowitz, J.2
Ferkinghoff-Borg, J.3
Stricher, F.4
Serrano, L.5
Rousseau, F.6
-
60
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modelling
-
Tegner J., Yeung M.K., Hasty J., and Collins J.J. Reverse engineering gene networks: Integrating genetic perturbations with dynamical modelling. Proc Natl Acad Sci USA 100 (2003) 5944-5949
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
|