-
1
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.-W. Hung, G.J. Kapral, and R.W. Grosse-Kunstleve PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkóczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.-W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
-
2
-
-
0027482857
-
Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation
-
M. Akke, N.J. Skelton, J. Kördel, A.G. Palmer 3rd, and W.J. Chazin Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation Biochemistry 32 1993 9832 9844
-
(1993)
Biochemistry
, vol.32
, pp. 9832-9844
-
-
Akke, M.1
Skelton, N.J.2
Kördel, J.3
Palmer III, A.G.4
Chazin, W.J.5
-
3
-
-
8544221118
-
Network analysis of protein structures identifies functional residues
-
G. Amitai, A. Shemesh, E. Sitbon, M. Shklar, D. Netanely, I. Venger, and S. Pietrokovski Network analysis of protein structures identifies functional residues J. Mol. Biol. 344 2004 1135 1146
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
Pietrokovski, S.7
-
4
-
-
0021504608
-
The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus)
-
P.J. Carter, G. Winter, A.J. Wilkinson, and A.R. Fersht The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus) Cell 38 1984 835 840
-
(1984)
Cell
, vol.38
, pp. 835-840
-
-
Carter, P.J.1
Winter, G.2
Wilkinson, A.J.3
Fersht, A.R.4
-
5
-
-
33845995427
-
Two conserved residues govern the salt and pH dependencies of the binding reaction of a PDZ domain
-
C.N. Chi, A. Engström, S. Gianni, M. Larsson, and P. Jemth Two conserved residues govern the salt and pH dependencies of the binding reaction of a PDZ domain J. Biol. Chem. 281 2006 36811 36818
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 36811-36818
-
-
Chi, C.N.1
Engström, A.2
Gianni, S.3
Larsson, M.4
Jemth, P.5
-
6
-
-
68049085520
-
A sequential binding mechanism in a PDZ domain
-
C.N. Chi, A. Bach, A. Engström, H.Q. Wang, K. Strømgaard, S. Gianni, and P. Jemth A sequential binding mechanism in a PDZ domain Biochemistry 48 2009 7089 7097
-
(2009)
Biochemistry
, vol.48
, pp. 7089-7097
-
-
Chi, C.N.1
Bach, A.2
Engström, A.3
Wang, H.Q.4
Strømgaard, K.5
Gianni, S.6
Jemth, P.7
-
7
-
-
84870707533
-
Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e
-
E. Cilia, G.W. Vuister, and T. Lenaerts Accurate prediction of the dynamical changes within the second PDZ domain of PTP1e PLoS Comput. Biol. 8 2012 e1002794
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. 1002794
-
-
Cilia, E.1
Vuister, G.W.2
Lenaerts, T.3
-
8
-
-
0021658956
-
Allostery without conformational change. A plausible model
-
A. Cooper, and D.T. Dryden Allostery without conformational change. A plausible model Eur. Biophys. J. 11 1984 103 109
-
(1984)
Eur. Biophys. J.
, vol.11
, pp. 103-109
-
-
Cooper, A.1
Dryden, D.T.2
-
9
-
-
55849106575
-
Efficient identification of critical residues based only on protein structure by network analysis
-
M.P. Cusack, B. Thibert, D.E. Bredesen, and G. Del Rio Efficient identification of critical residues based only on protein structure by network analysis PLoS ONE 2 2007 e421
-
(2007)
PLoS ONE
, vol.2
, pp. 421
-
-
Cusack, M.P.1
Thibert, B.2
Bredesen, D.E.3
Del Rio, G.4
-
10
-
-
47349099470
-
Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein
-
A. Dhulesia, J. Gsponer, and M. Vendruscolo Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein J. Am. Chem. Soc. 130 2008 8931 8939
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 8931-8939
-
-
Dhulesia, A.1
Gsponer, J.2
Vendruscolo, M.3
-
11
-
-
0030604722
-
Crystal structures of a complexed and peptide-free membrane protein-binding domain: Molecular basis of peptide recognition by PDZ
-
D.A. Doyle, A. Lee, J. Lewis, E. Kim, M. Sheng, and R. MacKinnon Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ Cell 85 1996 1067 1076
-
(1996)
Cell
, vol.85
, pp. 1067-1076
-
-
Doyle, D.A.1
Lee, A.2
Lewis, J.3
Kim, E.4
Sheng, M.5
Mackinnon, R.6
-
12
-
-
0026511656
-
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
-
A.R. Fersht, A. Matouschek, and L. Serrano The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding J. Mol. Biol. 224 1992 771 782
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
13
-
-
34447503697
-
Conformational entropy in molecular recognition by proteins
-
K.K. Frederick, M.S. Marlow, K.G. Valentine, and A.J. Wand Conformational entropy in molecular recognition by proteins Nature 448 2007 325 329
-
(2007)
Nature
, vol.448
, pp. 325-329
-
-
Frederick, K.K.1
Marlow, M.S.2
Valentine, K.G.3
Wand, A.J.4
-
14
-
-
0347753736
-
Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
-
E.J. Fuentes, C.J. Der, and A.L. Lee Ligand-dependent dynamics and intramolecular signaling in a PDZ domain J. Mol. Biol. 335 2004 1105 1115
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 1105-1115
-
-
Fuentes, E.J.1
Der, C.J.2
Lee, A.L.3
-
15
-
-
33750795402
-
Evaluation of energetic and dynamic coupling networks in a PDZ domain protein
-
E.J. Fuentes, S.A. Gilmore, R.V. Mauldin, and A.L. Lee Evaluation of energetic and dynamic coupling networks in a PDZ domain protein J. Mol. Biol. 364 2006 337 351
-
(2006)
J. Mol. Biol.
, vol.364
, pp. 337-351
-
-
Fuentes, E.J.1
Gilmore, S.A.2
Mauldin, R.V.3
Lee, A.L.4
-
16
-
-
80054804699
-
Allosteric communication in cysteinyl tRNA synthetase: A network of direct and indirect readout
-
A. Ghosh, R. Sakaguchi, C. Liu, S. Vishveshwara, and Y.-M. Hou Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout J. Biol. Chem. 286 2011 37721 37731
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 37721-37731
-
-
Ghosh, A.1
Sakaguchi, R.2
Liu, C.3
Vishveshwara, S.4
Hou, Y.-M.5
-
17
-
-
79961006047
-
Sequence specific long-range networks in PDZ domains tune their binding selectivity
-
S. Gianni, S.R. Haq, L. Montemiglio, M.C. Jürgens, Å. Engström, C.N. Chi, M. Brunori, and P. Jemth Sequence specific long-range networks in PDZ domains tune their binding selectivity J. Biol. Chem. 286 2011 27167 27175
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 27167-27175
-
-
Gianni, S.1
Haq, S.R.2
Montemiglio, L.3
Jürgens, M.C.4
Engström, A.5
Chi, C.N.6
Brunori, M.7
Jemth, P.8
-
18
-
-
84870336885
-
Protein structure networks
-
L.H. Greene Protein structure networks Brief Funct. Genomics 11 2012 469 478
-
(2012)
Brief Funct. Genomics
, vol.11
, pp. 469-478
-
-
Greene, L.H.1
-
19
-
-
77952913083
-
The plastic energy landscape of protein folding: A triangular folding mechanism with an equilibrium intermediate for a small protein domain
-
S.R. Haq, M.C. Jürgens, C.N. Chi, C.-S. Koh, L. Elfström, M. Selmer, S. Gianni, and P. Jemth The plastic energy landscape of protein folding: a triangular folding mechanism with an equilibrium intermediate for a small protein domain J. Biol. Chem. 285 2010 18051 18059
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 18051-18059
-
-
Haq, S.R.1
Jürgens, M.C.2
Chi, C.N.3
Koh, C.-S.4
Elfström, L.5
Selmer, M.6
Gianni, S.7
Jemth, P.8
-
20
-
-
84855656923
-
Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains
-
S.R. Haq, C.N. Chi, A. Bach, J. Dogan, A. Engström, G. Hultqvist, O.A. Karlsson, P. Lundström, L.C. Montemiglio, and K. Strømgaard Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains J. Am. Chem. Soc. 134 2012 599 605
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 599-605
-
-
Haq, S.R.1
Chi, C.N.2
Bach, A.3
Dogan, J.4
Engström, A.5
Hultqvist, G.6
Karlsson, O.A.7
Lundström, P.8
Montemiglio, L.C.9
Strømgaard, K.10
-
21
-
-
77249178809
-
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility
-
B.K. Ho, and D.A. Agard Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility Protein Sci. 19 2010 398 411
-
(2010)
Protein Sci.
, vol.19
, pp. 398-411
-
-
Ho, B.K.1
Agard, D.A.2
-
22
-
-
0030322783
-
Double-mutant cycles: A powerful tool for analyzing protein structure and function
-
A. Horovitz Double-mutant cycles: a powerful tool for analyzing protein structure and function Fold. Des. 1 1996 R121 R126
-
(1996)
Fold. Des.
, vol.1
-
-
Horovitz, A.1
-
23
-
-
34347326305
-
Ligand binding and circular permutation modify residue interaction network in DHFR
-
Z. Hu, D. Bowen, W.M. Southerland, A. del Sol, Y. Pan, R. Nussinov, and B. Ma Ligand binding and circular permutation modify residue interaction network in DHFR PLoS Comput. Biol. 3 2007 e117
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 117
-
-
Hu, Z.1
Bowen, D.2
Southerland, W.M.3
Del Sol, A.4
Pan, Y.5
Nussinov, R.6
Ma, B.7
-
24
-
-
84869796108
-
Tolerance of protein folding to a circular permutation in a PDZ domain
-
G. Hultqvist, A.S. Punekar, A. Morrone, C.N. Chi, Å. Engström, M. Selmer, S. Gianni, and P. Jemth Tolerance of protein folding to a circular permutation in a PDZ domain PLoS ONE 7 2012 e50055
-
(2012)
PLoS ONE
, vol.7
, pp. 50055
-
-
Hultqvist, G.1
Punekar, A.S.2
Morrone, A.3
Chi, C.N.4
Engström, A.5
Selmer, M.6
Gianni, S.7
Jemth, P.8
-
25
-
-
0033578690
-
Identification of side-chain clusters in protein structures by a graph spectral method
-
N. Kannan, and S. Vishveshwara Identification of side-chain clusters in protein structures by a graph spectral method J. Mol. Biol. 292 1999 441 464
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 441-464
-
-
Kannan, N.1
Vishveshwara, S.2
-
26
-
-
58949102247
-
Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis
-
Y. Kong, and M. Karplus Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis Proteins 74 2009 145 154
-
(2009)
Proteins
, vol.74
, pp. 145-154
-
-
Kong, Y.1
Karplus, M.2
-
27
-
-
69949152607
-
Conservation of side-chain dynamics within a protein family
-
A.B. Law, E.J. Fuentes, and A.L. Lee Conservation of side-chain dynamics within a protein family J. Am. Chem. Soc. 131 2009 6322 6323
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 6322-6323
-
-
Law, A.B.1
Fuentes, E.J.2
Lee, A.L.3
-
28
-
-
34648828242
-
Solution structure of the hDlg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 papillomavirus E6 protein
-
Y. Liu, G.D. Henry, R.S. Hegde, and J.D. Baleja Solution structure of the hDlg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 papillomavirus E6 protein Biochemistry 46 2007 10864 10874
-
(2007)
Biochemistry
, vol.46
, pp. 10864-10874
-
-
Liu, Y.1
Henry, G.D.2
Hegde, R.S.3
Baleja, J.D.4
-
29
-
-
70449808104
-
On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model
-
Z. Liu, J. Chen, and D. Thirumalai On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: illustrations using lattice model Proteins 77 2009 823 831
-
(2009)
Proteins
, vol.77
, pp. 823-831
-
-
Liu, Z.1
Chen, J.2
Thirumalai, D.3
-
30
-
-
82455220936
-
A Critical Evaluation of Correlated Mutation Algorithms and Coevolution Within Allosteric Mechanisms
-
A.W. Fenton, Springer New York
-
D.R. Livesay, K.E. Kreth, and A.A. Fodor A Critical Evaluation of Correlated Mutation Algorithms and Coevolution Within Allosteric Mechanisms A.W. Fenton, Allostery 2012 Springer New York 385 398
-
(2012)
Allostery
, pp. 385-398
-
-
Livesay, D.R.1
Kreth, K.E.2
Fodor, A.A.3
-
31
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
S.W. Lockless, and R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 286 1999 295 299
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
32
-
-
21844437963
-
The study of bimolecular reactions under non-pseudo-first order conditions
-
F. Malatesta The study of bimolecular reactions under non-pseudo-first order conditions Biophys. Chem. 116 2005 251 256
-
(2005)
Biophys. Chem.
, vol.116
, pp. 251-256
-
-
Malatesta, F.1
-
33
-
-
77951281285
-
The role of conformational entropy in molecular recognition by calmodulin
-
M.S. Marlow, J. Dogan, K.K. Frederick, K.G. Valentine, and A.J. Wand The role of conformational entropy in molecular recognition by calmodulin Nat. Chem. Biol. 6 2010 352 358
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 352-358
-
-
Marlow, M.S.1
Dogan, J.2
Frederick, K.K.3
Valentine, K.G.4
Wand, A.J.5
-
34
-
-
79960149420
-
RING: Networking interacting residues, evolutionary information and energetics in protein structures
-
A.J.M. Martin, M. Vidotto, F. Boscariol, T. Di Domenico, I. Walsh, and S.C.E. Tosatto RING: networking interacting residues, evolutionary information and energetics in protein structures Bioinformatics 27 2011 2003 2005
-
(2011)
Bioinformatics
, vol.27
, pp. 2003-2005
-
-
Martin, A.J.M.1
Vidotto, M.2
Boscariol, F.3
Di Domenico, T.4
Walsh, I.5
Tosatto, S.C.E.6
-
35
-
-
84879088309
-
Colocalization of fast and slow timescale dynamics in the allosteric signalling protein CheY
-
L.R. McDonald, M.J. Whitley, J.A. Boyer, and A.L. Lee Colocalization of fast and slow timescale dynamics in the allosteric signalling protein CheY J. Mol. Biol. 425 2013 2372 2381
-
(2013)
J. Mol. Biol.
, vol.425
, pp. 2372-2381
-
-
McDonald, L.R.1
Whitley, M.J.2
Boyer, J.A.3
Lee, A.L.4
-
36
-
-
84868365613
-
The spatial architecture of protein function and adaptation
-
R.N. McLaughlin Jr., F.J. Poelwijk, A. Raman, W.S. Gosal, and R. Ranganathan The spatial architecture of protein function and adaptation Nature 491 2012 138 142
-
(2012)
Nature
, vol.491
, pp. 138-142
-
-
McLaughlin, Jr.R.N.1
Poelwijk, F.J.2
Raman, A.3
Gosal, W.S.4
Ranganathan, R.5
-
37
-
-
0032055632
-
CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90
-
M. Niethammer, J.G. Valtschanoff, T.M. Kapoor, D.W. Allison, R.J. Weinberg, A.M. Craig, and M. Sheng CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90 Neuron 20 1998 693 707
-
(1998)
Neuron
, vol.20
, pp. 693-707
-
-
Niethammer, M.1
Valtschanoff, J.G.2
Kapoor, T.M.3
Allison, D.W.4
Weinberg, R.J.5
Craig, A.M.6
Sheng, M.7
-
38
-
-
22444450449
-
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
-
N. Ota, and D.A. Agard Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion J. Mol. Biol. 351 2005 345 354
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 345-354
-
-
Ota, N.1
Agard, D.A.2
-
41
-
-
33749029273
-
Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
-
K. Sharp, and J.J. Skinner Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling Proteins 65 2006 347 361
-
(2006)
Proteins
, vol.65
, pp. 347-361
-
-
Sharp, K.1
Skinner, J.J.2
-
42
-
-
79551587720
-
Cytoscape 2.8: New features for data integration and network visualization
-
M.E. Smoot, K. Ono, J. Ruscheinski, P.-L. Wang, and T. Ideker Cytoscape 2.8: new features for data integration and network visualization Bioinformatics 27 2011 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
-
43
-
-
35148894521
-
Predicting allosteric communication in myosin via a pathway of conserved residues
-
S. Tang, J.-C. Liao, A.R. Dunn, R.B. Altman, J.A. Spudich, and J.P. Schmidt Predicting allosteric communication in myosin via a pathway of conserved residues J. Mol. Biol. 373 2007 1361 1373
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 1361-1373
-
-
Tang, S.1
Liao, J.-C.2
Dunn, A.R.3
Altman, R.B.4
Spudich, J.A.5
Schmidt, J.P.6
-
44
-
-
70450191983
-
Dynamic activation of an allosteric regulatory protein
-
S.-R. Tzeng, and C.G. Kalodimos Dynamic activation of an allosteric regulatory protein Nature 462 2009 368 372
-
(2009)
Nature
, vol.462
, pp. 368-372
-
-
Tzeng, S.-R.1
Kalodimos, C.G.2
-
46
-
-
78649883885
-
Interaction energy based protein structure networks
-
M.S. Vijayabaskar, and S. Vishveshwara Interaction energy based protein structure networks Biophys. J. 99 2010 3704 3715
-
(2010)
Biophys. J.
, vol.99
, pp. 3704-3715
-
-
Vijayabaskar, M.S.1
Vishveshwara, S.2
-
47
-
-
0036300569
-
Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL
-
T. Walma, C.A.E.M. Spronk, M. Tessari, J. Aelen, J. Schepens, W. Hendriks, and G.W. Vuister Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL J. Mol. Biol. 316 2002 1101 1110
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 1101-1110
-
-
Walma, T.1
Spronk, C.A.E.M.2
Tessari, M.3
Aelen, J.4
Schepens, J.5
Hendriks, W.6
Vuister, G.W.7
-
48
-
-
84861194648
-
Extensions of PSD-95/discs large/ZO-1 (PDZ) domains influence lipid binding and membrane targeting of syntenin-1
-
A.M. Wawrzyniak, E. Vermeiren, P. Zimmermann, and Y. Ivarsson Extensions of PSD-95/discs large/ZO-1 (PDZ) domains influence lipid binding and membrane targeting of syntenin-1 FEBS Lett. 586 2012 1445 1451
-
(2012)
FEBS Lett.
, vol.586
, pp. 1445-1451
-
-
Wawrzyniak, A.M.1
Vermeiren, E.2
Zimmermann, P.3
Ivarsson, Y.4
-
49
-
-
78049307619
-
Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E
-
J. Zhang, P.J. Sapienza, H. Ke, A. Chang, S.R. Hengel, H. Wang, G.N. Phillips, and A.L. Lee Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E Biochemistry 49 2010 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
Wang, H.6
Phillips, G.N.7
Lee, A.L.8
|