-
1
-
-
84881493915
-
The spatial structure of cell signaling systems
-
R. Nussinov The spatial structure of cell signaling systems Phys. Biol. 2013 10 045004
-
(2013)
Phys. Biol.
, vol.10
, pp. 045004
-
-
Nussinov, R.1
-
2
-
-
84856340032
-
TranscriptomeBrowser 3.0: Introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
-
C. Lepoivre A. Bergon F. Lopez N. B. Perumal C. Nguyen J. Imbert D. Puthier TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks BMC Bioinformatics 2012 13 19
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 19
-
-
Lepoivre, C.1
Bergon, A.2
Lopez, F.3
Perumal, N.B.4
Nguyen, C.5
Imbert, J.6
Puthier, D.7
-
3
-
-
84889092648
-
PainNetworks: A web-based resource for the visualisation of pain-related genes in the context of their network associations
-
J. R. Perkins J. Lees A. Antunes-Martins I. Diboun S. B. McMahon D. L. Bennett C. Orengo PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations Pain 2013 154 2586
-
(2013)
Pain
, vol.154
, pp. 2586
-
-
Perkins, J.R.1
Lees, J.2
Antunes-Martins, A.3
Diboun, I.4
McMahon, S.B.5
Bennett, D.L.6
Orengo, C.7
-
4
-
-
79959715936
-
Four-dimensional visualisation and analysis of protein-protein interaction networks
-
A. Goel S. S. Li M. R. Wilkins Four-dimensional visualisation and analysis of protein-protein interaction networks Proteomics 2011 11 2672 2682
-
(2011)
Proteomics
, vol.11
, pp. 2672-2682
-
-
Goel, A.1
Li, S.S.2
Wilkins, M.R.3
-
5
-
-
78650373804
-
Network medicine: A network-based approach to human disease
-
A. L. Barabasi N. Gulbahce J. Loscalzo Network medicine: a network-based approach to human disease Nat. Rev. Genet. 2011 12 56 68
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 56-68
-
-
Barabasi, A.L.1
Gulbahce, N.2
Loscalzo, J.3
-
6
-
-
84861779036
-
Topological analysis and interactive visualization of biological networks and protein structures
-
N. T. Doncheva Y. Assenov F. S. Domingues M. Albrecht Topological analysis and interactive visualization of biological networks and protein structures Nat. Protoc. 2012 7 670 685
-
(2012)
Nat. Protoc.
, vol.7
, pp. 670-685
-
-
Doncheva, N.T.1
Assenov, Y.2
Domingues, F.S.3
Albrecht, M.4
-
8
-
-
34247580211
-
Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication
-
A. R. Atilgan D. Turgut C. Atilgan Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication Biophys. J. 2007 92 3052 3062
-
(2007)
Biophys. J.
, vol.92
, pp. 3052-3062
-
-
Atilgan, A.R.1
Turgut, D.2
Atilgan, C.3
-
9
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics
-
A. R. Atilgan P. Akan C. Baysal Small-world communication of residues and significance for protein dynamics Biophys. J. 2004 86 85 91
-
(2004)
Biophys. J.
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
10
-
-
41149167073
-
Structural identification of the pathway of long-range communication in an allosteric enzyme
-
P. S. Gandhi Z. Chen F. S. Mathews C. E. Di Structural identification of the pathway of long-range communication in an allosteric enzyme Proc. Natl. Acad. Sci. U. S. A. 2008 105 1832 1837
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 1832-1837
-
-
Gandhi, P.S.1
Chen, Z.2
Mathews, F.S.3
Di, C.E.4
-
12
-
-
84864205788
-
XPyder: A PyMOL plugin to analyze coupled residues and their networks in protein structures
-
M. Pasi M. Tiberti A. Arrigoni E. Papaleo xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures J. Chem. Inf. Model. 2012 52 1865 1874
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1865-1874
-
-
Pasi, M.1
Tiberti, M.2
Arrigoni, A.3
Papaleo, E.4
-
13
-
-
35648944297
-
A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
-
A. Ghosh S. Vishveshwara A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis Proc. Natl. Acad. Sci. U. S. A. 2007 104 15711 15716
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 15711-15716
-
-
Ghosh, A.1
Vishveshwara, S.2
-
14
-
-
80054804699
-
Allosteric communication in cysteinyl tRNA synthetase: A network of direct and indirect readout
-
A. Ghosh R. Sakaguchi C. Liu S. Vishveshwara Y. M. Hou Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout J. Biol. Chem. 2011 286 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
-
15
-
-
80053590126
-
Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases
-
A. Dixit G. M. Verkhivker Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases PLoS Comput. Biol. 2011 7 e1002179
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. 1002179
-
-
Dixit, A.1
Verkhivker, G.M.2
-
16
-
-
0345687171
-
A comparative study of motor-protein motions by using a simple elastic-network model
-
W. Zheng S. Doniach A comparative study of motor-protein motions by using a simple elastic-network model Proc. Natl. Acad. Sci. U. S. A. 2003 100 13253 13258
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, pp. 13253-13258
-
-
Zheng, W.1
Doniach, S.2
-
17
-
-
84899495170
-
PARS: A web server for the prediction of Protein Allosteric and Regulatory Sites
-
A. Panjkovich X. Daura PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites Bioinformatics 2014
-
(2014)
Bioinformatics
-
-
Panjkovich, A.1
Daura, X.2
-
20
-
-
46449101584
-
Discrete breathers in protein structures
-
F. Piazza Y. H. Sanejouand Discrete breathers in protein structures Phys. Biol. 2008 5 026001
-
(2008)
Phys. Biol.
, vol.5
, pp. 026001
-
-
Piazza, F.1
Sanejouand, Y.H.2
-
21
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
S. W. Lockless R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 1999 286 295 299
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
23
-
-
84861520898
-
Spatial regulation of receptor tyrosine kinases in development and cancer
-
J. B. Casaletto A. I. McClatchey Spatial regulation of receptor tyrosine kinases in development and cancer Nat. Rev. Cancer 2012 12 387 400
-
(2012)
Nat. Rev. Cancer
, vol.12
, pp. 387-400
-
-
Casaletto, J.B.1
McClatchey, A.I.2
-
24
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
J. Monod J. Wyman J. P. Changeux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 1965 12 88 118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
25
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
D. E. Koshland, Jr. G. Nemethy D. Filmer Comparison of experimental binding data and theoretical models in proteins containing subunits Biochemistry 1966 5 365 385
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland, D.E.1
Nemethy, G.2
Filmer, D.3
-
26
-
-
0014958182
-
Stereochemistry of cooperative effects in haemoglobin
-
M. F. Perutz Stereochemistry of cooperative effects in haemoglobin Nature 1970 228 726 739
-
(1970)
Nature
, vol.228
, pp. 726-739
-
-
Perutz, M.F.1
-
27
-
-
48249141040
-
Allostery and cooperativity revisited
-
Q. Cui M. Karplus Allostery and cooperativity revisited Protein Sci. 2008 17 1295 1307
-
(2008)
Protein Sci.
, vol.17
, pp. 1295-1307
-
-
Cui, Q.1
Karplus, M.2
-
28
-
-
60649109828
-
Protein allostery, signal transmission and dynamics: A classification scheme of allosteric mechanisms
-
C. Tsai J.; del, S. A.; Nussinov, R. Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms Mol. BioSyst. 2009 5 207 216
-
(2009)
Mol. BioSyst.
, vol.5
, pp. 207-216
-
-
Tsai, C.1
Del, S.A.2
Nussinov, R.3
-
29
-
-
84866079682
-
Allosteric communication across the native and mutated KIT receptor tyrosine kinase
-
E. Laine C. Auclair L. Tchertanov Allosteric communication across the native and mutated KIT receptor tyrosine kinase PLoS Comput. Biol. 2012 8 e1002661
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. 1002661
-
-
Laine, E.1
Auclair, C.2
Tchertanov, L.3
-
31
-
-
84863304598
-
-
R. Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team, R: A Language and Environment for Statistical Computing, 2013, R. Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0
-
(2013)
R: A Language and Environment for Statistical Computing
-
-
-
34
-
-
23444454552
-
The Amber biomolecular simulation programs
-
D. A. Case T. E. Cheatham T. Darden H. Gohlke R. Luo K. M. Merz A. Onufriev C. Simmerling B. Wang R. J. Woods The Amber biomolecular simulation programs J. Comput. Chem. 2005 26 1668 1688
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
35
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
S. Pronk S. Pall R. Schulz P. Larsson P. Bjelkmar R. Apostolov M. R. Shirts J. C. Smith P. M. Kasson D. van der Spoel B. Hess E. Lindahl GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 2013 29 7 845 854
-
(2013)
Bioinformatics
, vol.29
, Issue.7
, pp. 845-854
-
-
Pronk, S.1
Pall, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
Hess, B.11
Lindahl, E.12
-
36
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
I. K. Mcdonald J. M. Thornton Satisfying hydrogen bonding potential in proteins J. Mol. Biol. 1994 238 777 793
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
37
-
-
70450228871
-
Long-range energy transfer in proteins
-
F. Piazza Y. H. Sanejouand Long-range energy transfer in proteins Phys. Biol. 2009 6 046014
-
(2009)
Phys. Biol.
, vol.6
, pp. 046014
-
-
Piazza, F.1
Sanejouand, Y.H.2
-
38
-
-
0000209334
-
Local feture analysis: A general statistical theory for object representation
-
P. S. Penev J. J. Atick Local feture analysis: a general statistical theory for object representation Network: Comput. Neural Syst. 1996 7 477 500
-
(1996)
Network: Comput. Neural Syst.
, vol.7
, pp. 477-500
-
-
Penev, P.S.1
Atick, J.J.2
-
39
-
-
33745587301
-
Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules
-
Z. Y. Zhang W. Wriggers Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules Proteins: Struct., Funct., Bioinf. 2006 64 391 403
-
(2006)
Proteins: Struct., Funct., Bioinf.
, vol.64
, pp. 391-403
-
-
Zhang, Z.Y.1
Wriggers, W.2
-
40
-
-
41049092674
-
Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL
-
C. Chennubhotla Z. Yang I. Bahar Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL Mol. BioSyst. 2008 4 287 292
-
(2008)
Mol. BioSyst.
, vol.4
, pp. 287-292
-
-
Chennubhotla, C.1
Yang, Z.2
Bahar, I.3
-
41
-
-
63549104682
-
Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer
-
G. Morra G. Verkhivker G. Colombo Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer PLoS Comput. Biol. 2009 5 e1000323
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 1000323
-
-
Morra, G.1
Verkhivker, G.2
Colombo, G.3
-
42
-
-
34848882812
-
Signal propagation in proteins and relation to equilibrium fluctuations
-
C. Chennubhotla I. Bahar Signal propagation in proteins and relation to equilibrium fluctuations PLoS Comput. Biol. 2007 3 1716 1726
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 1716-1726
-
-
Chennubhotla, C.1
Bahar, I.2
-
43
-
-
79955479719
-
Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5
-
M. J. Abraham J. E. Gready Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5 J. Comput. Chem. 2011 32 2031 2040
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 2031-2040
-
-
Abraham, M.J.1
Gready, J.E.2
-
44
-
-
0035902180
-
Oncogenic kinase signalling
-
P. Blume-Jensen T. Hunter Oncogenic kinase signalling Nature 2001 411 355 365
-
(2001)
Nature
, vol.411
, pp. 355-365
-
-
Blume-Jensen, P.1
Hunter, T.2
-
45
-
-
0037013143
-
The conformational plasticity of protein kinases
-
M. Huse J. Kuriyan The conformational plasticity of protein kinases Cell 2002 109 275 282
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
46
-
-
77953896432
-
Cell Signaling by Receptor Tyrosine Kinases
-
M. A. Lemmon J. Schlessinger Cell Signaling by Receptor Tyrosine Kinases Cell 2010 141 1117 1134
-
(2010)
Cell
, vol.141
, pp. 1117-1134
-
-
Lemmon, M.A.1
Schlessinger, J.2
-
47
-
-
0034693799
-
The protein tyrosine kinase family of the human genome
-
D. R. Robinson Y. M. Wu S. F. Lin The protein tyrosine kinase family of the human genome Oncogene 2000 19 5548 5557
-
(2000)
Oncogene
, vol.19
, pp. 5548-5557
-
-
Robinson, D.R.1
Wu, Y.M.2
Lin, S.F.3
-
48
-
-
0025343230
-
Signal transduction by receptors with tyrosine kinase activity
-
A. Ullrich J. Schlessinger Signal transduction by receptors with tyrosine kinase activity Cell 1990 61 203 212
-
(1990)
Cell
, vol.61
, pp. 203-212
-
-
Ullrich, A.1
Schlessinger, J.2
-
49
-
-
79953215678
-
Mechanisms of STAT protein activation by oncogenic KIT mutants in neoplastic mast cells
-
A. Chaix S. Lopez E. Voisset L. Gros P. Dubreuil S. P. De Mechanisms of STAT protein activation by oncogenic KIT mutants in neoplastic mast cells J. Biol. Chem. 2011 286 5956 5966
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 5956-5966
-
-
Chaix, A.1
Lopez, S.2
Voisset, E.3
Gros, L.4
Dubreuil, P.5
De, S.P.6
-
50
-
-
4444353636
-
Regulation of protein kinases; Controlling activity through activation segment conformation
-
B. Nolen S. Taylor G. Ghosh Regulation of protein kinases; controlling activity through activation segment conformation Mol. Cell 2004 15 661 675
-
(2004)
Mol. Cell
, vol.15
, pp. 661-675
-
-
Nolen, B.1
Taylor, S.2
Ghosh, G.3
-
51
-
-
0038731316
-
Juxtamembrane mutant V560GKit is more sensitive to Imatinib (STI571) compared with wild-type c-kit whereas the kinase domain mutant D816VKit is resistant
-
M. J. Frost P. T. Ferrao T. P. Hughes L. K. Ashman Juxtamembrane mutant V560GKit is more sensitive to Imatinib (STI571) compared with wild-type c-kit whereas the kinase domain mutant D816VKit is resistant Mol. Cancer Ther. 2002 1 1115 1124
-
(2002)
Mol. Cancer Ther.
, vol.1
, pp. 1115-1124
-
-
Frost, M.J.1
Ferrao, P.T.2
Hughes, T.P.3
Ashman, L.K.4
-
52
-
-
84908113203
-
Characterization of S628N, a novel KIT mutation found in a metastatic melanoma
-
accepted
-
M. Vita J. Tisserand I. Chauvot de Beauchêne N. Panel L. Tchertanov J. Agopian L. Mascam-Mancini B. Fouet B. Fournier P. Dubreuil F. Bertucci P. De Sepulveda Characterization of S628N, a novel KIT mutation found in a metastatic melanoma JAMA Derm. 2014
-
(2014)
JAMA Derm.
-
-
Vita, M.1
Tisserand, J.2
Chauvot De Beauchêne, I.3
Panel, N.4
Tchertanov, L.5
Agopian, J.6
Mascam-Mancini, L.7
Fouet, B.8
Fournier, B.9
Dubreuil, P.10
Bertucci, F.11
De Sepulveda, P.12
-
53
-
-
79959833426
-
Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
-
E. Laine d. B. I. Chauvot D. Perahia C. Auclair L. Tchertanov Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms PLoS Comput. Biol. 2011 7 e1002068
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. 1002068
-
-
Laine, E.1
Chauvot, D.B.I.2
Perahia, D.3
Auclair, C.4
Tchertanov, L.5
-
54
-
-
84905474723
-
Hotspot mutations in KIT receptor differentially modulate its allosteric regulation: Impact on activation and drug sensitivity
-
resubmitted after revision
-
I. Chauvot de Beauchêne A. Allain E. Laine P. Dubreuil L. Tchertanov Hotspot mutations in KIT receptor differentially modulate its allosteric regulation: impact on activation and drug sensitivity PLoS Comput. Biol. 2014
-
(2014)
PLoS Comput. Biol.
-
-
Chauvot De Beauchêne, I.1
Allain, A.2
Laine, E.3
Dubreuil, P.4
Tchertanov, L.5
-
55
-
-
84901325169
-
Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication
-
P. Da Silva Figueiredo Celestino Gomes N. Panel E. Laine P. G. Pascutti E. Solary L. Tchertanov Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication PLoS One 2014 9 5 e97519
-
(2014)
PLoS One
, vol.9
, Issue.5
, pp. 97519
-
-
Da Silva Figueiredo Celestino Gomes, P.1
Panel, N.2
Laine, E.3
Pascutti, P.G.4
Solary, E.5
Tchertanov, L.6
-
56
-
-
0032831735
-
Stat5a and Stat5b: Fraternal twins of signal transduction and transcriptional activation
-
P. M. Grimley F. Dong H. Rui Stat5a and Stat5b: fraternal twins of signal transduction and transcriptional activation Cytokine Growth Factor Rev. 1999 10 131 157
-
(1999)
Cytokine Growth Factor Rev.
, vol.10
, pp. 131-157
-
-
Grimley, P.M.1
Dong, F.2
Rui, H.3
-
57
-
-
9244243110
-
STATs as critical mediators of signal transduction and transcription: Lessons learned from STAT5
-
K. Paukku O. Silvennoinen STATs as critical mediators of signal transduction and transcription: lessons learned from STAT5 Cytokine Growth Factor Rev. 2004 15 435 455
-
(2004)
Cytokine Growth Factor Rev.
, vol.15
, pp. 435-455
-
-
Paukku, K.1
Silvennoinen, O.2
|