-
1
-
-
34249910312
-
Network analysis of protein dynamics
-
Böde C, Kovács IA, Szalay MS, Palotai R, Korcsmáros T, et al. (2007) Network analysis of protein dynamics. FEBS Lett 581: 2776-2782.
-
(2007)
FEBS Lett
, vol.581
, pp. 2776-2782
-
-
Böde, C.1
Kovács, I.A.2
Szalay, M.S.3
Palotai, R.4
Korcsmáros, T.5
-
2
-
-
84875170915
-
Protein contact networks: an emerging paradigm in chemistry
-
Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A, (2013) Protein contact networks: an emerging paradigm in chemistry. Chem Rev 113: 1598-1613.
-
(2013)
Chem Rev
, vol.113
, pp. 1598-1613
-
-
Di Paola, L.1
De Ruvo, M.2
Paci, P.3
Santoni, D.4
Giuliani, A.5
-
3
-
-
65649089458
-
Intra and inter-molecular communications through protein structure network
-
Vishveshwara S, Ghosh A, Hansia P, (2009) Intra and inter-molecular communications through protein structure network. Curr Protein Pept Sci 10: 146-160.
-
(2009)
Curr Protein Pept Sci
, vol.10
, pp. 146-160
-
-
Vishveshwara, S.1
Ghosh, A.2
Hansia, P.3
-
4
-
-
79960149420
-
RING: networking interacting residues, evolutionary information and energetics in protein structures
-
Martin AJM, Vidotto M, Boscariol F, Di Domenico T, Walsh I, et al. (2011) RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 27: 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
-
5
-
-
79954415213
-
Analyzing and visualizing residue networks of protein structures
-
Doncheva NT, Klein K, Domingues FS, Albrecht M, (2011) Analyzing and visualizing residue networks of protein structures. Trends Biochem Sci 36: 179-182.
-
(2011)
Trends Biochem Sci
, vol.36
, pp. 179-182
-
-
Doncheva, N.T.1
Klein, K.2
Domingues, F.S.3
Albrecht, M.4
-
6
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabási A-L, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
7
-
-
84874947727
-
The BioGRID interaction database: 2013 update
-
Chatr-Aryamontri A, Breitkreutz B-J, Heinicke S, Boucher L, Winter A, et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res 41: D816-D823.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.-J.2
Heinicke, S.3
Boucher, L.4
Winter, A.5
-
8
-
-
78651324347
-
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-D568.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
-
9
-
-
0036088133
-
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
-
Xenarios I, (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
-
10
-
-
72849142731
-
Edgetic perturbation models of human inherited disorders
-
Zhong Q, Simonis N, Li Q-R, Charloteaux B, Heuze F, et al. (2009) Edgetic perturbation models of human inherited disorders. Mol Syst Biol 5: 321.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 321
-
-
Zhong, Q.1
Simonis, N.2
Li, Q.-R.3
Charloteaux, B.4
Heuze, F.5
-
11
-
-
65649138753
-
Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design
-
Antal MA, Böde C, Csermely P, (2009) Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. Curr Protein Pept Sci 10: 161-172.
-
(2009)
Curr Protein Pept Sci
, vol.10
, pp. 161-172
-
-
Antal, M.A.1
Böde, C.2
Csermely, P.3
-
12
-
-
80555139635
-
Implicit methods for qualitative modeling of gene regulatory networks
-
Garg A, Mohanram K, De Micheli G, Xenarios I, (2012) Implicit methods for qualitative modeling of gene regulatory networks. Methods Mol Biol 786: 397-443.
-
(2012)
Methods Mol Biol
, vol.786
, pp. 397-443
-
-
Garg, A.1
Mohanram, K.2
De Micheli, G.3
Xenarios, I.4
-
13
-
-
79953109968
-
Elementary signaling modes predict the essentiality of signal transduction network components
-
Wang R-S, Albert R, (2011) Elementary signaling modes predict the essentiality of signal transduction network components. BMC Syst Biol 5: 44.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 44
-
-
Wang, R.-S.1
Albert, R.2
-
14
-
-
36248971654
-
Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments
-
Gong Y, Zhang Z, (2007) Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments. Ann N Y Acad Sci 1115: 267-285.
-
(2007)
Ann N Y Acad Sci
, vol.1115
, pp. 267-285
-
-
Gong, Y.1
Zhang, Z.2
-
15
-
-
36249005452
-
CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks
-
Gong Y, Zhang Z, (2007) CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks. Ann N Y Acad Sci 1115: 249-266.
-
(2007)
Ann N Y Acad Sci
, vol.1115
, pp. 249-266
-
-
Gong, Y.1
Zhang, Z.2
-
16
-
-
0036772705
-
Gene perturbation and intervention in probabilistic Boolean networks
-
Shmulevich I, Dougherty ER, Zhang W, (2002) Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics 18: 1319-1331.
-
(2002)
Bioinformatics
, vol.18
, pp. 1319-1331
-
-
Shmulevich, I.1
Dougherty, E.R.2
Zhang, W.3
-
17
-
-
69849111694
-
ITM Probe: analyzing information flow in protein networks
-
Stojmirovi A, Yu Y-K, Stojmirović A, (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics 25: 2447-2449.
-
(2009)
Bioinformatics
, vol.25
, pp. 2447-2449
-
-
Stojmirovi, A.1
Yu, Y.-K.2
Stojmirović, A.3
-
18
-
-
77950491448
-
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks
-
Li F, Li P, Xu W, Peng Y, Bo X, et al. (2010) PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. Bioinformatics 26: 275-277.
-
(2010)
Bioinformatics
, vol.26
, pp. 275-277
-
-
Li, F.1
Li, P.2
Xu, W.3
Peng, Y.4
Bo, X.5
-
19
-
-
33747877324
-
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
-
Calzone L, Fages F, Soliman S, (2006) BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22: 1805-1807.
-
(2006)
Bioinformatics
, vol.22
, pp. 1805-1807
-
-
Calzone, L.1
Fages, F.2
Soliman, S.3
-
20
-
-
84859348190
-
Conedy: a scientific tool to investigate complex network dynamics
-
Rothkegel A, Lehnertz K, (2012) Conedy: a scientific tool to investigate complex network dynamics. Chaos 22: 013125.
-
(2012)
Chaos
, vol.22
, pp. 013125
-
-
Rothkegel, A.1
Lehnertz, K.2
-
21
-
-
79956334133
-
Network-based tools for the identification of novel drug targets
-
Farkas IJ, Korcsmáros T, Kovács IA, Mihalik Á, Palotai R, et al. (2011) Network-based tools for the identification of novel drug targets. Sci Signal 4: pt3.
-
(2011)
Sci Signal
, vol.4
-
-
Farkas, I.J.1
Korcsmáros, T.2
Kovács, I.A.3
Mihalik, Á.4
Palotai, R.5
-
22
-
-
0035394703
-
Dynamics of complex systems above the glass temperature
-
De Almeida RMC, Lemke N, Jund P, Jullien R, Campbell IA, et al. (2001) Dynamics of complex systems above the glass temperature. J Non-Cryst Solids 287: 201-209.
-
(2001)
J Non-Cryst Solids
, vol.287
, pp. 201-209
-
-
De Almeida, R.M.C.1
Lemke, N.2
Jund, P.3
Jullien, R.4
Campbell, I.A.5
-
23
-
-
35348813628
-
Propagation of large concentration changes in reversible protein-binding networks
-
Maslov S, Ispolatov I, (2007) Propagation of large concentration changes in reversible protein-binding networks. Proc Natl Acad Sci U S A 104: 13655-13660.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 13655-13660
-
-
Maslov, S.1
Ispolatov, I.2
-
24
-
-
34247960076
-
The strength of weak ties
-
Granovetter M, (1973) The strength of weak ties. Am J Sociol 78: 1360-1380.
-
(1973)
Am J Sociol
, vol.78
, pp. 1360-1380
-
-
Granovetter, M.1
-
26
-
-
77549087023
-
Percolation and epidemics in random clustered networks
-
Miller JC, (2009) Percolation and epidemics in random clustered networks. Phys Rev E 80: 020901.
-
(2009)
Phys Rev E
, vol.80
, pp. 020901
-
-
Miller, J.C.1
-
27
-
-
40949115417
-
Impact of community structure on information transfer
-
Danon L, Arenas A, Díaz-Guilera A, (2008) Impact of community structure on information transfer. Phys Rev E 77: 036103.
-
(2008)
Phys Rev E
, vol.77
, pp. 036103
-
-
Danon, L.1
Arenas, A.2
Díaz-Guilera, A.3
-
28
-
-
68949111730
-
Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities
-
Lancichinetti A, Fortunato S, (2009) Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities. Phys Rev E 80: 016118.
-
(2009)
Phys Rev E
, vol.80
, pp. 016118
-
-
Lancichinetti, A.1
Fortunato, S.2
-
29
-
-
77958564958
-
Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics
-
Kovács IA, Palotai R, Szalay MS, Csermely P, (2010) Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics. PLoS ONE 5: e12528.
-
(2010)
PLoS ONE
, vol.5
-
-
Kovács, I.A.1
Palotai, R.2
Szalay, M.S.3
Csermely, P.4
-
31
-
-
48349116091
-
Extremism propagation in social networks with hubs
-
Franks DW, Noble J, Kaufmann P, Stagl S, (2008) Extremism propagation in social networks with hubs. Adapt Behav 16: 264-274.
-
(2008)
Adapt Behav
, vol.16
, pp. 264-274
-
-
Franks, D.W.1
Noble, J.2
Kaufmann, P.3
Stagl, S.4
-
33
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
Guimerà R, Nunes Amaral LA, (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimerà, R.1
Nunes Amaral, L.A.2
-
34
-
-
42949165604
-
Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases
-
Palotai R, Szalay MS, Csermely P, (2008) Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 60: 10-18.
-
(2008)
IUBMB Life
, vol.60
, pp. 10-18
-
-
Palotai, R.1
Szalay, M.S.2
Csermely, P.3
-
35
-
-
80055081144
-
Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation
-
Mihalik Á, Csermely P, (2011) Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. PLoS Comput Biol 7: e1002187.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Mihalik, Á.1
Csermely, P.2
-
36
-
-
0032567081
-
Dissecting the regulatory circuitry of a eukaryotic genome
-
Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.
-
(1998)
Cell
, vol.95
, pp. 717-728
-
-
Holstege, F.C.1
Jennings, E.G.2
Wyrick, J.J.3
Lee, T.I.4
Hengartner, C.J.5
-
37
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
-
38
-
-
79959923522
-
g:Profiler - a web server for functional interpretation of gene lists (2011 update)
-
Reimand J, Arak T, Vilo J, (2011) g:Profiler - a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res 39: W307-W315.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Reimand, J.1
Arak, T.2
Vilo, J.3
-
39
-
-
0028878281
-
Alterations in carbohydrate metabolism during stress: a review of the literature
-
Mizock BA, (1995) Alterations in carbohydrate metabolism during stress: a review of the literature. Am J Med 98: 75-84.
-
(1995)
Am J Med
, vol.98
, pp. 75-84
-
-
Mizock, B.A.1
-
40
-
-
0019433557
-
Regulation of protein synthesis during heat shock
-
Lindquist S, (1981) Regulation of protein synthesis during heat shock. Nature 293: 311-314.
-
(1981)
Nature
, vol.293
, pp. 311-314
-
-
Lindquist, S.1
-
41
-
-
58049164511
-
Boolean network simulations for life scientists
-
Albert I, Thakar J, Li S, Zhang R, Albert R, (2008) Boolean network simulations for life scientists. Source Code Biol Med 3: 16.
-
(2008)
Source Code Biol Med
, vol.3
, pp. 16
-
-
Albert, I.1
Thakar, J.2
Li, S.3
Zhang, R.4
Albert, R.5
-
42
-
-
0015514970
-
Will a large complex systembe stable?
-
May R, (1972) Will a large complex systembe stable? Nature 238: 413-414.
-
(1972)
Nature
, vol.238
, pp. 413-414
-
-
May, R.1
-
43
-
-
35648944297
-
A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
-
Ghosh A, Vishveshwara S, (2007) A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc Natl Acad Sci U S A 104: 15711-15716.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 15711-15716
-
-
Ghosh, A.1
Vishveshwara, S.2
-
44
-
-
77957231785
-
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
-
Csermely P, Palotai R, Nussinov R, (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 35: 539-546.
-
(2010)
Trends Biochem Sci
, vol.35
, pp. 539-546
-
-
Csermely, P.1
Palotai, R.2
Nussinov, R.3
-
45
-
-
66149086947
-
Dynamical networks in tRNA:protein complexes
-
Sethi A, Eargle J, Black AA, Luthey-Schulten Z, (2009) Dynamical networks in tRNA:protein complexes. Proc Natl Acad Sci U S A 106: 6620-6625.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 6620-6625
-
-
Sethi, A.1
Eargle, J.2
Black, A.A.3
Luthey-Schulten, Z.4
-
46
-
-
34248332629
-
Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble
-
Liu T, Whitten ST, Hilser VJ, (2007) Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble. Proc Natl Acad Sci U S A 104: 4347-4352.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 4347-4352
-
-
Liu, T.1
Whitten, S.T.2
Hilser, V.J.3
-
47
-
-
46449101584
-
Discrete breathers in protein structures
-
Piazza F, Sanejouand Y-H, (2008) Discrete breathers in protein structures. Phys Biol 5: 026001.
-
(2008)
Phys Biol
, vol.5
, pp. 026001
-
-
Piazza, F.1
Sanejouand, Y.-H.2
-
48
-
-
33847377573
-
A robustness-based approach to systems-oriented drug design
-
Kitano H, (2007) A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 6: 202-210.
-
(2007)
Nat Rev Drug Discov
, vol.6
, pp. 202-210
-
-
Kitano, H.1
-
49
-
-
81355154050
-
Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
-
Saadatpour A, Wang R-S, Liao A, Liu X, Loughran TP, et al. (2011) Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol 7: e1002267.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Saadatpour, A.1
Wang, R.-S.2
Liao, A.3
Liu, X.4
Loughran, T.P.5
-
50
-
-
15044349115
-
The efficiency of multi-target drugs: the network approach might help drug design
-
Csermely P, Ágoston V, Pongor S, (2005) The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci 26: 178-182.
-
(2005)
Trends Pharmacol Sci
, vol.26
, pp. 178-182
-
-
Csermely, P.1
Ágoston, V.2
Pongor, S.3
-
51
-
-
81755184126
-
Allo-network drugs: harnessing allostery in cellular networks
-
Nussinov R, Tsai C-J, Csermely P, (2011) Allo-network drugs: harnessing allostery in cellular networks. Trends Pharmacol Sci 32: 686-693.
-
(2011)
Trends Pharmacol Sci
, vol.32
, pp. 686-693
-
-
Nussinov, R.1
Tsai, C.-J.2
Csermely, P.3
-
52
-
-
84877580262
-
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
-
Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R, (2013) Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacol Ther 138: 333-408.
-
(2013)
Pharmacol Ther
, vol.138
, pp. 333-408
-
-
Csermely, P.1
Korcsmáros, T.2
Kiss, H.J.M.3
London, G.4
Nussinov, R.5
-
53
-
-
36048944020
-
Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks
-
Behar M, Dohlman HG, Elston TC, (2007) Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks. Proc Natl Acad Sci U S A 104: 16146-16151.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 16146-16151
-
-
Behar, M.1
Dohlman, H.G.2
Elston, T.C.3
-
54
-
-
0003509593
-
-
3rd ed. Sedra AS, Lightner MR, New York: Oxford University Press
-
Chen C-T (1998) Linear System Theory and Design. 3rd ed. Sedra AS, Lightner MR, New York: Oxford University Press.
-
(1998)
Linear System Theory and Design
-
-
Chen, C.-T.1
-
55
-
-
0345687195
-
An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution
-
Scott EE, He YA, Wester MR, White MA, Chin CC, et al. (2003) An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution. Proc Natl Acad Sci U S A 100: 13196-13201.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 13196-13201
-
-
Scott, E.E.1
He, Y.A.2
Wester, M.R.3
White, M.A.4
Chin, C.C.5
-
56
-
-
3042553224
-
Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding
-
Scott EE, White MA, He YA, Johnson EF, Stout CD, et al. (2004) Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding. J Biol Chem 279: 27294-27301.
-
(2004)
J Biol Chem
, vol.279
, pp. 27294-27301
-
-
Scott, E.E.1
White, M.A.2
He, Y.A.3
Johnson, E.F.4
Stout, C.D.5
-
59
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal Complex Systems: 1695.
-
(2006)
InterJournal Complex Systems
, pp. 1695
-
-
Csardi, G.1
Nepusz, T.2
|