-
1
-
-
0031171361
-
PDZ domains: targeting signalling molecules to sub-membranous sites
-
Ponting CP, Phillips C, Davies KE, Blake DJ, (1997) PDZ domains: targeting signalling molecules to sub-membranous sites. BioEssays 19: 469-479.
-
(1997)
BioEssays
, vol.19
, pp. 469-479
-
-
Ponting, C.P.1
Phillips, C.2
Davies, K.E.3
Blake, D.J.4
-
3
-
-
0347753736
-
Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
-
Fuentes EJ, Der CJ, Lee AL, (2004) Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. Journal of molecular biology 335: 1105-1115.
-
(2004)
Journal of Molecular Biology
, vol.335
, pp. 1105-1115
-
-
Fuentes, E.J.1
Der, C.J.2
Lee, A.L.3
-
4
-
-
33845186553
-
Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering
-
Gianni S, Walma T, Arcovito A, Calosci N, Bellelli A, et al. (2006) Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering. Structure 14: 1801-1809.
-
(2006)
Structure
, vol.14
, pp. 1801-1809
-
-
Gianni, S.1
Walma, T.2
Arcovito, A.3
Calosci, N.4
Bellelli, A.5
-
5
-
-
70849084011
-
Hidden dynamic allostery in a PDZ domain
-
Petit CM, Zhang J, Sapienza PJ, Fuentes EJ, Lee AL, (2009) Hidden dynamic allostery in a PDZ domain. Proceedings of the National Academy of Sciences of the United States of America 106: 18249-18254.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 18249-18254
-
-
Petit, C.M.1
Zhang, J.2
Sapienza, P.J.3
Fuentes, E.J.4
Lee, A.L.5
-
6
-
-
1642276423
-
Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition
-
Peterson FC, Penkert RR, Volkman BF, Prehoda KE, (2004) Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition. Molecular cell 13: 665-676.
-
(2004)
Molecular Cell
, vol.13
, pp. 665-676
-
-
Peterson, F.C.1
Penkert, R.R.2
Volkman, B.F.3
Prehoda, K.E.4
-
7
-
-
36749069824
-
An allosteric intramolecular PDZ-PDZ interaction modulates PTP-BL PDZ2 binding specificity
-
van den Berk LC, Landi E, Walma T, Vuister GW, Dente L, et al. (2007) An allosteric intramolecular PDZ-PDZ interaction modulates PTP-BL PDZ2 binding specificity. Biochemistry 46: 13629-13637.
-
(2007)
Biochemistry
, vol.46
, pp. 13629-13637
-
-
van den Berk, L.C.1
Landi, E.2
Walma, T.3
Vuister, G.W.4
Dente, L.5
-
8
-
-
65649100094
-
Frameworks for understanding long-range intra-protein communication
-
Whitley MJ, Lee AL, (2009) Frameworks for understanding long-range intra-protein communication. Current protein & peptide science 10: 116-127.
-
(2009)
Current Protein & Peptide Science
, vol.10
, pp. 116-127
-
-
Whitley, M.J.1
Lee, A.L.2
-
11
-
-
60649109828
-
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms
-
Tsai CJ, Del Sol A, Nussinov R, (2009) Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Molecular bioSystems 5: 207-216.
-
(2009)
Molecular BioSystems
, vol.5
, pp. 207-216
-
-
Tsai, C.J.1
Del Sol, A.2
Nussinov, R.3
-
12
-
-
64849111005
-
Sending signals dynamically
-
Smock RG, Gierasch LM, (2009) Sending signals dynamically. Science 324: 198-203.
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
13
-
-
41149104308
-
Allostery: absence of a change in shape does not imply that allostery is not at play
-
Tsai CJ, del Sol A, Nussinov R, (2008) Allostery: absence of a change in shape does not imply that allostery is not at play. Journal of molecular biology 378: 1-11.
-
(2008)
Journal of Molecular Biology
, vol.378
, pp. 1-11
-
-
Tsai, C.J.1
del Sol, A.2
Nussinov, R.3
-
15
-
-
6344219895
-
Is allostery an intrinsic property of all dynamic proteins?
-
Gunasekaran K, Ma B, Nussinov R, (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57: 433-443.
-
(2004)
Proteins
, vol.57
, pp. 433-443
-
-
Gunasekaran, K.1
Ma, B.2
Nussinov, R.3
-
16
-
-
76249122268
-
Biochemistry. An ensemble view of allostery
-
Hilser VJ, (2010) Biochemistry. An ensemble view of allostery. Science 327: 653-654.
-
(2010)
Science
, vol.327
, pp. 653-654
-
-
Hilser, V.J.1
-
17
-
-
78049307619
-
Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E
-
Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, et al. (2010) Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Biochemistry 49: 9280-9291.
-
(2010)
Biochemistry
, vol.49
, pp. 9280-9291
-
-
Zhang, J.1
Sapienza, P.J.2
Ke, H.3
Chang, A.4
Hengel, S.R.5
-
18
-
-
33750795402
-
Evaluation of energetic and dynamic coupling networks in a PDZ domain protein
-
Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL, (2006) Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. Journal of molecular biology 364: 337-351.
-
(2006)
Journal of Molecular Biology
, vol.364
, pp. 337-351
-
-
Fuentes, E.J.1
Gilmore, S.A.2
Mauldin, R.V.3
Lee, A.L.4
-
20
-
-
58949102247
-
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis
-
Kong Y, Karplus M, (2009) Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins 74: 145-154.
-
(2009)
Proteins
, vol.74
, pp. 145-154
-
-
Kong, Y.1
Karplus, M.2
-
21
-
-
80055066238
-
Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
-
Gerek ZN, Ozkan SB, (2011) Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning. PLoS computational biology 7: e1002154.
-
(2011)
PLoS Computational Biology
, vol.7
-
-
Gerek, Z.N.1
Ozkan, S.B.2
-
22
-
-
68749107059
-
Protein sectors: evolutionary units of three-dimensional structure
-
Halabi N, Rivoire O, Leibler S, Ranganathan R, (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell 138: 774-786.
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
23
-
-
0034646395
-
Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor
-
Kozlov G, Gehring K, Ekiel I, (2000) Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor. Biochemistry 39: 2572-2580.
-
(2000)
Biochemistry
, vol.39
, pp. 2572-2580
-
-
Kozlov, G.1
Gehring, K.2
Ekiel, I.3
-
24
-
-
0036301446
-
Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions
-
Kozlov G, Banville D, Gehring K, Ekiel I, (2002) Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions. Journal of molecular biology 320: 813-820.
-
(2002)
Journal of Molecular Biology
, vol.320
, pp. 813-820
-
-
Kozlov, G.1
Banville, D.2
Gehring, K.3
Ekiel, I.4
-
25
-
-
47349099470
-
Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein
-
Dhulesia A, Gsponer J, Vendruscolo M, (2008) Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein. Journal of the American Chemical Society 130: 8931-8939.
-
(2008)
Journal of the American Chemical Society
, vol.130
, pp. 8931-8939
-
-
Dhulesia, A.1
Gsponer, J.2
Vendruscolo, M.3
-
26
-
-
56549131325
-
Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure
-
Lenaerts T, Ferkinghoff-Borg J, Stricher F, Serrano L, Schymkowitz JW, et al. (2008) Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC structural biology 8: 43.
-
(2008)
BMC Structural Biology
, vol.8
, pp. 43
-
-
Lenaerts, T.1
Ferkinghoff-Borg, J.2
Stricher, F.3
Serrano, L.4
Schymkowitz, J.W.5
-
27
-
-
0036300569
-
Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL
-
Walma T, Spronk CA, Tessari M, Aelen J, Schepens J, et al. (2002) Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL. Journal of molecular biology 316: 1101-1110.
-
(2002)
Journal of Molecular Biology
, vol.316
, pp. 1101-1110
-
-
Walma, T.1
Spronk, C.A.2
Tessari, M.3
Aelen, J.4
Schepens, J.5
-
28
-
-
80053443092
-
Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone
-
Dubay KH, Bothma JP, Geissler PL, (2011) Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone. PLoS computational biology 7: e1002168.
-
(2011)
PLoS Computational Biology
, vol.7
-
-
Dubay, K.H.1
Bothma, J.P.2
Geissler, P.L.3
-
29
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless SW, Ranganathan R, (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
30
-
-
0036301446
-
Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta 2-beta 3 loop to PDZ domain-ligand interactions
-
Kozlov G, Banville D, Gehring K, Ekiel I, (2002) Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta 2-beta 3 loop to PDZ domain-ligand interactions. Journal of molecular biology 320: 813-820.
-
(2002)
Journal of Molecular Biology
, vol.320
, pp. 813-820
-
-
Kozlov, G.1
Banville, D.2
Gehring, K.3
Ekiel, I.4
-
31
-
-
0034646395
-
Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptors
-
Kozlov G, Gehring K, Ekiel I, (2000) Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptors. Biochemistry 39: 2572-2580.
-
(2000)
Biochemistry
, vol.39
, pp. 2572-2580
-
-
Kozlov, G.1
Gehring, K.2
Ekiel, I.3
-
32
-
-
10344223464
-
Making optimal use of empirical energy functions: Force-field parameterization in crystal space
-
Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G, (2004) Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins-Structure Function and Bioinformatics 57: 678-683.
-
(2004)
Proteins-Structure Function and Bioinformatics
, vol.57
, pp. 678-683
-
-
Krieger, E.1
Darden, T.2
Nabuurs, S.B.3
Finkelstein, A.4
Vriend, G.5
-
33
-
-
0025398721
-
WHAT IF: a molecular modeling and drug design program
-
29
-
Vriend G, (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8: 52-56, 29.
-
(1990)
J Mol Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
34
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L, (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. Journal of molecular biology 320: 369-387.
-
(2002)
Journal of Molecular Biology
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
35
-
-
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
-
37
-
-
58149195307
-
Discretization for naive-Bayes learning: managing discretization bias and variance
-
Yang Y, Webb GI, (2009) Discretization for naive-Bayes learning: managing discretization bias and variance. Machine Learning 74: 39-74.
-
(2009)
Machine Learning
, vol.74
, pp. 39-74
-
-
Yang, Y.1
Webb, G.I.2
-
39
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
Watts DJ, Strogatz SH, (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
40
-
-
12944331889
-
Small-world network approach to identify key residues in protein-protein interaction
-
del Sol A, O'Meara P, (2005) Small-world network approach to identify key residues in protein-protein interaction. Proteins 58: 672-682.
-
(2005)
Proteins
, vol.58
, pp. 672-682
-
-
del Sol, A.1
O'Meara, P.2
-
41
-
-
33745461893
-
Residues crucial for maintaining short paths in network communication mediate signaling in proteins
-
2006 0019
-
del Sol A, Fujihashi H, Amoros D, Nussinov R, (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular systems biology 2: 2006 0019.
-
(2006)
Molecular Systems Biology
, vol.2
-
-
del Sol, A.1
Fujihashi, H.2
Amoros, D.3
Nussinov, R.4
-
42
-
-
33746218852
-
MUSTANG: a multiple structural alignment algorithm
-
Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM, (2006) MUSTANG: a multiple structural alignment algorithm. Proteins 64: 559-574.
-
(2006)
Proteins
, vol.64
, pp. 559-574
-
-
Konagurthu, A.S.1
Whisstock, J.C.2
Stuckey, P.J.3
Lesk, A.M.4
-
43
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. Journal of computational chemistry 25: 1605-1612.
-
(2004)
Journal of Computational Chemistry
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
-
44
-
-
79551587720
-
Cytoscape 2.8: new features for data integration and network visualization
-
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
-
(2011)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
Wang, P.L.4
Ideker, T.5
|