-
1
-
-
0030950608
-
Modular peptide recognition domains in eukaryotic signaling
-
Kuriyan J, Cowburn D (1997) Modular peptide recognition domains in eukaryotic signaling. Annu Rev Biophys Biomol Struct 26: 259-288.
-
(1997)
Annu Rev Biophys Biomol Struct
, vol.26
, pp. 259-288
-
-
Kuriyan, J.1
Cowburn, D.2
-
2
-
-
2542463049
-
Selectivity and promiscuity in the interaction network mediated by protein recognition modules
-
Castagnoli L, Costantini A, Dall'Armi C, Gonfloni S, Montecchi-Palazzi L, et al. (2004) Selectivity and promiscuity in the interaction network mediated by protein recognition modules. FEBS Lett 567: 74-79.
-
(2004)
FEBS Lett
, vol.567
, pp. 74-79
-
-
Castagnoli, L.1
Costantini, A.2
Dall'Armi, C.3
Gonfloni, S.4
Montecchi-Palazzi, L.5
-
3
-
-
0029006062
-
The Multiplicity of Domains in Proteins
-
Doolittle RF (1995) The Multiplicity of Domains in Proteins. Annual Review of Biochemistry 64: 287-314.
-
(1995)
Annual Review of Biochemistry
, vol.64
, pp. 287-314
-
-
Doolittle, R.F.1
-
4
-
-
38549153238
-
Data growth and its impact on the SCOP database: New developments
-
Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJP, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36: D419-425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.-M.3
Brenner, S.E.4
Hubbard, T.J.P.5
-
6
-
-
0033601076
-
Shroom, a PDZ domain-containing actinbinding protein, is required for neural tube morphogenesis in mice
-
Hildebrand J, Soriano P (1999) Shroom, a PDZ domain-containing actinbinding protein, is required for neural tube morphogenesis in mice. Cell 99: 485-497.
-
(1999)
Cell
, vol.99
, pp. 485-497
-
-
Hildebrand, J.1
Soriano, P.2
-
7
-
-
0033816925
-
A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C
-
Verpy E, Leibovici M, Zwaenepoel I, Liu X-Z, Gal A, et al. (2000) A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C. Nat Genet 26: 51-55.
-
(2000)
Nat Genet
, vol.26
, pp. 51-55
-
-
Verpy, E.1
Leibovici, M.2
Zwaenepoel, I.3
Liu, X.-Z.4
Gal, A.5
-
8
-
-
15644379801
-
Recognition of Unique Carboxyl-Terminal Motifs by Distinct PDZ Domains
-
Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, et al. (1997) Recognition of Unique Carboxyl-Terminal Motifs by Distinct PDZ Domains. Science 275: 73-77.
-
(1997)
Science
, vol.275
, pp. 73-77
-
-
Songyang, Z.1
Fanning, A.S.2
Fu, C.3
Xu, J.4
Marfatia, S.M.5
-
9
-
-
0034740693
-
Mechanism and role of PDZ domains in signaling complex assembly
-
Harris BZ, Lim WA (2001) Mechanism and role of PDZ domains in signaling complex assembly. J Cell Sci 114: 3219-3231.
-
(2001)
J Cell Sci
, vol.114
, pp. 3219-3231
-
-
Harris, B.Z.1
Lim, W.A.2
-
10
-
-
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
-
11
-
-
70450065485
-
Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behaviour
-
Gerek ZN, Keskin O, Ozkan SB (2009) Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behaviour. Proteins 77: 796-811.
-
(2009)
Proteins
, vol.77
, pp. 796-811
-
-
Gerek, Z.N.1
Keskin, O.2
Ozkan, S.B.3
-
12
-
-
33749511033
-
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study
-
Basdevant N, Weinstein H, Ceruso M (2006) Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc 128: 12766-12777.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 12766-12777
-
-
Basdevant, N.1
Weinstein, H.2
Ceruso, M.3
-
13
-
-
0035861856
-
Classification of PDZ domains
-
Bezprozvanny I, Maximov A (2001) Classification of PDZ domains. FEBS Lett 509: 457-462.
-
(2001)
FEBS Lett
, vol.509
, pp. 457-462
-
-
Bezprozvanny, I.1
Maximov, A.2
-
14
-
-
54749086397
-
A Specificity Map for the PDZ Domain Family
-
Tonikian R, Sazinsky S, Currell B, Yeh J, Reva B, et al. (2008) A Specificity Map for the PDZ Domain Family. Plos Biol 6: e239.
-
(2008)
Plos Biol
, vol.6
-
-
Tonikian, R.1
Sazinsky, S.2
Currell, B.3
Yeh, J.4
Reva, B.5
-
16
-
-
34548737494
-
Insights into the molecular evolution of the PDZ-LIM family and indentification of a novel conserved protein motif
-
te Velthuis AJW, Isogai T, Gerrits L, Bagowski CP (2007) Insights into the molecular evolution of the PDZ-LIM family and indentification of a novel conserved protein motif. PLOS ONE 2: e189.
-
(2007)
PLOS ONE
, vol.2
-
-
te Velthuis, A.J.W.1
Isogai, T.2
Gerrits, L.3
Bagowski, C.P.4
-
17
-
-
51349085386
-
Predicting PDZ domain-peptide interactions from primary sequences
-
Chen JR, Chang BH, Allen JE, Stiffler MA, MacBeath G (2008) Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotech 26: 1041-1045.
-
(2008)
Nat Biotech
, vol.26
, pp. 1041-1045
-
-
Chen, J.R.1
Chang, B.H.2
Allen, J.E.3
Stiffler, M.A.4
McBeath, G.5
-
18
-
-
0037449799
-
Novel mode of ligand recognition by Erbin PDZ domain
-
Birrane G, Chung J, Ladias JAA (2002) Novel mode of ligand recognition by Erbin PDZ domain. J Biol Chem 278: 1399-1402.
-
(2002)
J Biol Chem
, vol.278
, pp. 1399-1402
-
-
Birrane, G.1
Chung, J.2
Ladias, J.A.A.3
-
19
-
-
0037470140
-
Structure determination and mutagenesis of the erbin PDZ domain
-
Skelton NJ, Koehler MFT, Zobel K, Wong WL, Yeh S, et al. (2003) Structure determination and mutagenesis of the erbin PDZ domain. J Biol Chem 278: 7645-7654.
-
(2003)
J Biol Chem
, vol.278
, pp. 7645-7654
-
-
Skelton, N.J.1
Koehler, M.F.T.2
Zobel, K.3
Wong, W.L.4
Yeh, S.5
-
20
-
-
33644877451
-
SMART 5: Domains in the context of genomes and networks
-
Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, et al. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34: D257-260.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Letunic, I.1
Copley, R.R.2
Pils, B.3
Pinkert, S.4
Schultz, J.5
-
22
-
-
77951612635
-
Evolutionary expansion and specialization of the PDZ domains
-
doi:10.1093/ molbev/msp311
-
Sakarya O, Conaco C, Egecioglu O, Solla SA, Oakley TH, et al. (2009) Evolutionary expansion and specialization of the PDZ domains. Mol Biol Evol. doi:10.1093/ molbev/msp311.
-
(2009)
Mol Biol Evol
-
-
Sakarya, O.1
Conaco, C.2
Egecioglu, O.3
Solla, S.A.4
Oakley, T.H.5
-
23
-
-
0033823061
-
Crystal structures of the photosystem II D1 C-terminal processing protease
-
Liao DI, Qian J, Chisholm DA, Jordan DB, Diner BA (2000) Crystal structures of the photosystem II D1 C-terminal processing protease. Nat Struct Biol 7: 749-753.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 749-753
-
-
Liao, D.I.1
Qian, J.2
Chisholm, D.A.3
Jordan, D.B.4
Diner, B.A.5
-
24
-
-
58049199407
-
A pair of circularly permutated PDZ domains control RseP, the S2P family intramembrane protease of Escherichia coli
-
Inaba K, Suzuki M, Maegawa K, Akiyama S, Ito K, et al. (2008) A pair of circularly permutated PDZ domains control RseP, the S2P family intramembrane protease of Escherichia coli. J Biol Chem 283: 35042-35052.
-
(2008)
J Biol Chem
, vol.283
, pp. 35042-35052
-
-
Inaba, K.1
Suzuki, M.2
Maegawa, K.3
Akiyama, S.4
Ito, K.5
-
25
-
-
44049089395
-
Folding and misfolding in a naturally occurring circularly permuted PDZ domain
-
Ivarsson Y, Travaglini-Allocatelli C, Brunori M, Gianni S (2008) Folding and misfolding in a naturally occurring circularly permuted PDZ domain. J Biol Chem 283: 8954-8960.
-
(2008)
J Biol Chem
, vol.283
, pp. 8954-8960
-
-
Ivarsson, Y.1
Travaglini-Allocatelli, C.2
Brunori, M.3
Gianni, S.4
-
26
-
-
65549111825
-
Domain mobility in proteins: Functional and evolutionary implications
-
Basu MK, Poliakov E, Rogozin IB (2009) Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform 10: 205-216.
-
(2009)
Brief Bioinform
, vol.10
, pp. 205-216
-
-
Basu, M.K.1
Poliakov, E.2
Rogozin, I.B.3
-
27
-
-
67649221640
-
Domain Interaction Footprint: A multi-classification approach to predict domain-peptide interactions
-
Schillinger C, Boisguerin P, Krause G (2009) Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions. Bioinformatics 25: 1632-1639.
-
(2009)
Bioinformatics
, vol.25
, pp. 1632-1639
-
-
Schillinger, C.1
Boisguerin, P.2
Krause, G.3
-
28
-
-
4744353840
-
Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides
-
Wiedemann U, Boisguerin P, Leber R, Leitner D, Krause G, et al. (2004) Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J Mol Biol 343: 703-718.
-
(2004)
J Mol Biol
, vol.343
, pp. 703-718
-
-
Wiedemann, U.1
Boisguerin, P.2
Leber, R.3
Leitner, D.4
Krause, G.5
-
29
-
-
77954044144
-
Interaction prediction and classificatio of PDZ domains
-
Kalyoncu S, Keskin O, Gursoy A (2010) Interaction prediction and classificatio of PDZ domains. BMC Bioinformatics 11: 357.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 357
-
-
Kalyoncu, S.1
Keskin, O.2
Gursoy, A.3
-
30
-
-
77957737014
-
Proteome scanning to predict PDZ domain interactions using support vector machines
-
Hui S, Bader GD (2010) Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinformatics 11: 507.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 507
-
-
Hui, S.1
Bader, G.D.2
-
31
-
-
0042622380
-
SWISS-MODEL: An automated protein homology-modeling server
-
Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31: 3381-3385.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3381-3385
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.C.4
-
32
-
-
34249653071
-
Towards zoomable multidimensional maps of the cell
-
Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, et al. (2007) Towards zoomable multidimensional maps of the cell. Nat Biotech 25: 547-554.
-
(2007)
Nat Biotech
, vol.25
, pp. 547-554
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
Kanehisa, M.4
Stuart, J.M.5
-
33
-
-
45849099864
-
Linking fold function and phylogeny: A Comparative Genomics View on Protein (Domain) Evolution
-
te Velthuis AJW, Bagowski CP (2008) Linking fold function and phylogeny: A Comparative Genomics View on Protein (Domain) Evolution. Current Genomics 9: 88-96.
-
(2008)
Current Genomics
, vol.9
, pp. 88-96
-
-
te Velthuis, A.J.W.1
Bagowski, C.P.2
-
34
-
-
58549092371
-
Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density
-
Feng W, Zhang M (2009) Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density. Nat Rev Neurosci 10: 87-99.
-
(2009)
Nat Rev Neurosci
, vol.10
, pp. 87-99
-
-
Feng, W.1
Zhang, M.2
-
35
-
-
0037493100
-
Organization of Signaling Complexes by PDZDomain Scaffold Proteins
-
Zhang M, Wang W (2003) Organization of Signaling Complexes by PDZDomain Scaffold Proteins. Accounts of Chemical Research 36: 530-538.
-
(2003)
Accounts of Chemical Research
, vol.36
, pp. 530-538
-
-
Zhang, M.1
Wang, W.2
-
36
-
-
0033529567
-
Regulation of DLG Localization at Synapses by CaMKII-Dependent Phosphorylation
-
Koh YH, Popova E, Thomas U, Griffith LC, Budnik V (1999) Regulation of DLG Localization at Synapses by CaMKII-Dependent Phosphorylation. Cell 98: 353-363.
-
(1999)
Cell
, vol.98
, pp. 353-363
-
-
Koh, Y.H.1
Popova, E.2
Thomas, U.3
Griffith, L.C.4
Budnik, V.5
-
37
-
-
59249091710
-
A Class III PDZ Binding Motif in the Myotilin and FATZ Families Binds Enigma Family Proteins: A Common Link for Z-Disc Myopathies
-
von Nandelstadh P, Ismail M, Gardin C, Suila H, Zara I, et al. (2009) A Class III PDZ Binding Motif in the Myotilin and FATZ Families Binds Enigma Family Proteins: a Common Link for Z-Disc Myopathies. Mol Cell Biol 29: 822-834.
-
(2009)
Mol Cell Biol
, vol.29
, pp. 822-834
-
-
von Nandelstadh, P.1
Ismail, M.2
Gardin, C.3
Suila, H.4
Zara, I.5
-
38
-
-
0037023742
-
Phosphorylation of Stargazin by Protein Kinase A Regulates Its Interaction with PSD-95
-
Choi J, Ko J, Park E, Lee J-R, Yoon J, et al. (2002) Phosphorylation of Stargazin by Protein Kinase A Regulates Its Interaction with PSD-95. J Biol Chem 277: 12359-12363.
-
(2002)
J Biol Chem
, vol.277
, pp. 12359-12363
-
-
Choi, J.1
Ko, J.2
Park, E.3
Lee, J.-R.4
Yoon, J.5
-
39
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 1792-1797.
-
(2004)
Nucl Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
40
-
-
0000122573
-
PHYLIP - Phylogeny Inference Package (Version 3.2)
-
Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
41
-
-
0033753685
-
Visualizing large hierarchical clusters in hyperbolic space
-
Bingham J, Sudarsanam S (2000) Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics 16: 660-661.
-
(2000)
Bioinformatics
, vol.16
, pp. 660-661
-
-
Bingham, J.1
Sudarsanam, S.2
-
42
-
-
10044222704
-
CLANS: A Java application for visualizing protein families based on pairwise similarity
-
Frickey T, Lupas A (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20: 3702-3704.
-
(2004)
Bioinformatics
, vol.20
, pp. 3702-3704
-
-
Frickey, T.1
Lupas, A.2
-
43
-
-
14844294424
-
Protein production by auto-induction in high density shaking cultures
-
Studier F (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207-234.
-
(2005)
Protein Expr Purif
, vol.41
, pp. 207-234
-
-
Studier, F.1
-
44
-
-
33646679140
-
Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays
-
Stiffler MA, Grantcharova VP, Sevecka M, MacBeath G (2006) Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays. J Am Chem Soc 128: 5913-5922.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 5913-5922
-
-
Stiffler, M.A.1
Grantcharova, V.P.2
Sevecka, M.3
McBeath, G.4
-
45
-
-
0034069495
-
Gene Ontology: Tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
46
-
-
0141504252
-
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655
-
Gerdes S, Scholle M, Campbell J, Balázsi G, Ravasz E, et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185: 5673-5684.
-
(2003)
J Bacteriol
, vol.185
, pp. 5673-5684
-
-
Gerdes, S.1
Scholle, M.2
Campbell, J.3
Balázsi, G.4
Ravasz, E.5
-
47
-
-
4744353840
-
Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides
-
Wiedemann U, Boisguerin P, Leben R, Leitner D, Krause G, et al. (2004) Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J Mol Biol 343: 703-718.
-
(2004)
J Mol Biol
, vol.343
, pp. 703-718
-
-
Wiedemann, U.1
Boisguerin, P.2
Leben, R.3
Leitner, D.4
Krause, G.5
|