-
1
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 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
-
2
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 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
-
3
-
-
33644550021
-
Structural systems biology: Modelling protein interactions
-
Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7: 188-197.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 188-197
-
-
Aloy, P.1
Russell, R.B.2
-
4
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (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
-
5
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti P, Janin J (2002) Dissecting protein-protein recognition sites. Proteins 47: 331-343.
-
(2002)
Proteins
, vol.47
, pp. 331-343
-
-
Chakrabarti, P.1
Janin, J.2
-
6
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300: 445 452.
-
(2003)
Science
, vol.300
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
7
-
-
33744814686
-
Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms
-
Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, et al. (2006) Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci U S A 103: 8390-8395.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 8390-8395
-
-
Romero, P.R.1
Zaidi, S.2
Fang, Y.Y.3
Uversky, V.N.4
Radivojac, P.5
-
8
-
-
0036803243
-
Intrinsically unstructured proteins
-
Tompa P (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27: 527-533.
-
(2002)
Trends Biochem Sci
, vol.27
, pp. 527-533
-
-
Tompa, P.1
-
9
-
-
24044540256
-
Specificity and versatility of SH3 and other proline-recognition domains: Structural basis and implications for cellular signal transduction
-
Li SS (2005) Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction. Biochem J 390: 641-653.
-
(2005)
Biochem J
, vol.390
, pp. 641-653
-
-
Li, S.S.1
-
10
-
-
19344377539
-
Protein interaction networks by proteome peptide scanning
-
Landgraf C, Panni S, Montecchi-Palazzi L, Castagnoli L, Schneider-Mergener J, et al. (2004) Protein interaction networks by proteome peptide scanning. PLoS Biol 2: E14.
-
(2004)
PLoS Biol
, vol.2
-
-
Landgraf, C.1
Panni, S.2
Montecchi-Palazzi, L.3
Castagnoli, L.4
Schneider-Mergener, J.5
-
11
-
-
20144372620
-
High-throughput mapping of a dynamic signaling network in mammalian cells
-
Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, et al. (2005) High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307: 1621-1625.
-
(2005)
Science
, vol.307
, pp. 1621-1625
-
-
Barrios-Rodiles, M.1
Brown, K.R.2
Ozdamar, B.3
Bose, R.4
Liu, Z.5
-
12
-
-
14844321287
-
Synthetic modular systems-reverse engineering of signal transduction
-
Pawson T, Linding R (2005) Synthetic modular systems-reverse engineering of signal transduction. FEBS Lett 579: 1808-1814.
-
(2005)
FEBS Lett
, vol.579
, pp. 1808-1814
-
-
Pawson, T.1
Linding, R.2
-
13
-
-
0042622252
-
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
-
Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, et al. (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31: 3625-3630.
-
(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
-
14
-
-
0346555269
-
Optimization of specificity in a cellular protein interaction network by negative selection
-
Zarrinpar A, Park SH, Lim WA (2003) Optimization of specificity in a cellular protein interaction network by negative selection. Nature 426: 676-680.
-
(2003)
Nature
, vol.426
, pp. 676-680
-
-
Zarrinpar, A.1
Park, S.H.2
Lim, W.A.3
-
15
-
-
34547127612
-
PDZ domain binding selectivity is optimized across the mouse proteome
-
Stiffler MA, Chen JR, Grantcharova VP, Lei Y, Fuchs D, et al. (2007) PDZ domain binding selectivity is optimized across the mouse proteome. Science 317: 364-369.
-
(2007)
Science
, vol.317
, pp. 364-369
-
-
Stiffler, M.A.1
Chen, J.R.2
Grantcharova, V.P.3
Lei, Y.4
Fuchs, D.5
-
16
-
-
34250743173
-
Systematic discovery of in vivo phosphorylation networks
-
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jorgensen C, et al. (2007) Systematic discovery of in vivo phosphorylation networks. Cell 129: 1415-1426.
-
(2007)
Cell
, vol.129
, pp. 1415-1426
-
-
Linding, R.1
Jensen, L.J.2
Ostheimer, G.J.3
van Vugt, M.A.4
Jorgensen, C.5
-
17
-
-
0037112758
-
Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules
-
Freund C, Kuhne R, Yang H, Park S, Reinherz EL, et al. (2002) Dynamic interaction of CD2 with the GYF and the SH3 domain of compartmentalized effector molecules. Embo J 21: 5985-5995.
-
(2002)
Embo J
, vol.21
, pp. 5985-5995
-
-
Freund, C.1
Kuhne, R.2
Yang, H.3
Park, S.4
Reinherz, E.L.5
-
18
-
-
0035863048
-
Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen
-
Kim HY, Ahn BY, Cho Y (2001) Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen. Embo J 20: 295-304.
-
(2001)
Embo J
, vol.20
, pp. 295-304
-
-
Kim, H.Y.1
Ahn, B.Y.2
Cho, Y.3
-
19
-
-
0034665266
-
Dual epitope recognition by the VASP EVH1 domain modulates polyproline ligand specificity and binding affinity
-
Ball LJ, Kuhne R, Hoffmann B, Hafner A, Schmieder P, et al. (2000) Dual epitope recognition by the VASP EVH1 domain modulates polyproline ligand specificity and binding affinity. Embo J 19: 4903-4914.
-
(2000)
Embo J
, vol.19
, pp. 4903-4914
-
-
Ball, L.J.1
Kuhne, R.2
Hoffmann, B.3
Hafner, A.4
Schmieder, P.5
-
20
-
-
0032213219
-
Structure and specificity of nuclear receptor-coactivator interactions
-
Darimont BD, Wagner RL, Apriletti JW, Stallcup MR, Kushner PJ, et al. (1998) Structure and specificity of nuclear receptor-coactivator interactions. Genes Dev 12: 3343-3356.
-
(1998)
Genes Dev
, vol.12
, pp. 3343-3356
-
-
Darimont, B.D.1
Wagner, R.L.2
Apriletti, J.W.3
Stallcup, M.R.4
Kushner, P.J.5
-
21
-
-
0033638454
-
The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms
-
Durocher D, Taylor IA, Sarbassova D, Haire LF, Westcott SL, et al. (2000) The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms. Mol Cell 6: 1169-1182.
-
(2000)
Mol Cell
, vol.6
, pp. 1169-1182
-
-
Durocher, D.1
Taylor, I.A.2
Sarbassova, D.3
Haire, L.F.4
Westcott, S.L.5
-
22
-
-
33645011914
-
Sequential phosphorylation and multisite interactions characterize specific target recognition by the FHA domain of Ki67
-
Byeon IJ, Li H, Song H, Gronenborn AM, Tsai MD (2005) Sequential phosphorylation and multisite interactions characterize specific target recognition by the FHA domain of Ki67. Nat Struct Mol Biol 12: 987-993.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 987-993
-
-
Byeon, I.J.1
Li, H.2
Song, H.3
Gronenborn, A.M.4
Tsai, M.D.5
-
23
-
-
27144492267
-
FHA domain-ligand interactions: Importance of integrating chemical and biological approaches
-
Mahajan A, Yuan C, Pike BL, Heierhorst J, Chang CF, et al. (2005) FHA domain-ligand interactions: importance of integrating chemical and biological approaches. J Am Chem Soc 127: 14572-14573.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 14572-14573
-
-
Mahajan, A.1
Yuan, C.2
Pike, B.L.3
Heierhorst, J.4
Chang, C.F.5
-
24
-
-
3042547846
-
Structural basis of protein phosphatase 1 regulation
-
Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R (2004) Structural basis of protein phosphatase 1 regulation. Nature 429: 780-784.
-
(2004)
Nature
, vol.429
, pp. 780-784
-
-
Terrak, M.1
Kerff, F.2
Langsetmo, K.3
Tao, T.4
Dominguez, R.5
-
25
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, 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
-
26
-
-
0033197872
-
The structural basis for the recognition of diverse receptor sequences by TRAF2
-
Ye H, Park YC, Kreishman M, Kieff E, Wu H (1999) The structural basis for the recognition of diverse receptor sequences by TRAF2. Mol Cell 4: 321-330.
-
(1999)
Mol Cell
, vol.4
, pp. 321-330
-
-
Ye, H.1
Park, Y.C.2
Kreishman, M.3
Kieff, E.4
Wu, H.5
-
27
-
-
22844450110
-
Systematic interpretation of genetic interactions using protein networks
-
Kelley R, Ideker T (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23: 561-566.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 561-566
-
-
Kelley, R.1
Ideker, T.2
-
28
-
-
34247193051
-
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
-
Ulitsky I, Shamir R (2007) Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol 3: 104.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 104
-
-
Ulitsky, I.1
Shamir, R.2
-
29
-
-
0034733912
-
Ligand-protein interactions in nuclear receptors of hormones
-
Egea PF, Klaholz BP, Moras D (2000) Ligand-protein interactions in nuclear receptors of hormones. FEBS Lett 476: 62 67.
-
(2000)
FEBS Lett
, vol.476
, pp. 62-67
-
-
Egea, P.F.1
Klaholz, B.P.2
Moras, D.3
-
30
-
-
0031833450
-
The nuclear receptor ligand-binding domain: Structure and function
-
Moras D, Gronemeyer H (1998) The nuclear receptor ligand-binding domain: structure and function. Curr Opin Cell Biol 10: 384-391.
-
(1998)
Curr Opin Cell Biol
, vol.10
, pp. 384-391
-
-
Moras, D.1
Gronemeyer, H.2
-
31
-
-
33845966382
-
The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor alpha ligand-binding domain
-
Folkertsma S, van Noort PI, de Heer A, Carati P, Brandt R, el al. (2007) The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor alpha ligand-binding domain. Mol Endocrinol 21: 30-48.
-
(2007)
Mol Endocrinol
, vol.21
, pp. 30-48
-
-
Folkertsma, S.1
van Noort, P.I.2
de Heer, A.3
Carati, P.4
Brandt, R.5
el al6
-
32
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci U S A 99: 5896-5901.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
33
-
-
13844293072
-
Recognizing and defining true Ras binding domains H: In silico prediction based on homology modelling and energy calculations
-
Kiel C, Wohlgemuth S, Rousseau F, Schymkowitz J, Ferkinghoff-Borg J, et al. (2005) Recognizing and defining true Ras binding domains H: in silico prediction based on homology modelling and energy calculations. J Mol Biol 34: 759-775.
-
(2005)
J Mol Biol
, vol.34
, pp. 759-775
-
-
Kiel, C.1
Wohlgemuth, S.2
Rousseau, F.3
Schymkowitz, J.4
Ferkinghoff-Borg, J.5
-
35
-
-
33748953868
-
Peptides mediating interaction networks: New leads at last
-
Neduva V, Russell RB (2006) Peptides mediating interaction networks: new leads at last. Curr Opin Biotechnol 17: 465 471.
-
(2006)
Curr Opin Biotechnol
, vol.17
, pp. 465-471
-
-
Neduva, V.1
Russell, R.B.2
-
36
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-251.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
-
37
-
-
0036291145
-
Predicting changes in de stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in de stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320: 369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
38
-
-
23144436398
-
The FoldX web server: An online force field
-
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, et al. (2005) The FoldX web server: an online force field. Nucleic Acids Res 33: W382-388.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
-
39
-
-
34250186793
-
A genomewide Ras-effector interaction network
-
Kiel C, Foglierini M, Kuemmerer N, Beltrao P, Serrano L (2007) A genomewide Ras-effector interaction network. J Mol Biol 370: 1020-1032.
-
(2007)
J Mol Biol
, vol.370
, pp. 1020-1032
-
-
Kiel, C.1
Foglierini, M.2
Kuemmerer, N.3
Beltrao, P.4
Serrano, L.5
-
40
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawlik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369: 1318 1332.
-
(2007)
J Mol Biol
, vol.369
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawlik, D.S.5
-
41
-
-
0034843597
-
AL2CO: Calculation of positional conservation in a protein sequence alignment
-
Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment Bioinformatics 17: 700-712.
-
(2001)
Bioinformatics
, vol.17
, pp. 700-712
-
-
Pei, J.1
Grishin, N.V.2
-
42
-
-
0026743174
-
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
-
Russell RB, Barton GJ (1992) Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14: 309-323.
-
(1992)
Proteins
, vol.14
, pp. 309-323
-
-
Russell, R.B.1
Barton, G.J.2
-
43
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 44-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 44-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
44
-
-
0029901637
-
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
-
Felsenstein J (1996) Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266: 418-427.
-
(1996)
Methods Enzymol
, vol.266
, pp. 418-427
-
-
Felsenstein, J.1
|