-
1
-
-
0038718854
-
The structure and function of complex networks
-
Newman M (2003) The structure and function of complex networks. SIAM Rev 45:167-256.
-
(2003)
SIAM Rev
, vol.45
, pp. 167-256
-
-
Newman, M.1
-
4
-
-
84870315927
-
Local motifs in proteins combine to generate global functional moves
-
Atilgan AR, Atilgan C (2012) Local motifs in proteins combine to generate global functional moves. Brief Funct Genomics 11:479-488.
-
(2012)
Brief Funct Genomics
, vol.11
, pp. 479-488
-
-
Atilgan, A.R.1
Atilgan, C.2
-
5
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene LH, Higman VA (2003) Uncovering network systems within protein structures. J Mol Biol 334:781-791.
-
(2003)
J Mol Biol
, vol.334
, pp. 781-791
-
-
Greene, L.H.1
Higman, V.A.2
-
6
-
-
0033578690
-
Identification of side-Chain clusters in protein structures by a graph spectral method
-
Kannan N, Vishveshwara S (1999) Identification of side-Chain clusters in protein structures by a graph spectral method. J Mol Biol 292:441-464.
-
(1999)
J Mol Biol
, vol.292
, pp. 441-464
-
-
Kannan, N.1
Vishveshwara, S.2
-
7
-
-
79955670187
-
Network approach for capturing ligand-Induced subtle global changes in protein structures
-
Sukhwal A, Bhattacharyya M, Vishveshwara S (2011) Network approach for capturing ligand-Induced subtle global changes in protein structures. Acta Cryst D67:429-439.
-
(2011)
Acta Cryst
, vol.D67
, pp. 429-439
-
-
Sukhwal, A.1
Bhattacharyya, M.2
Vishveshwara, S.3
-
8
-
-
77949907106
-
Allostery and conformational free energy changes in human tryptophanyl-TRNA synthetase from essential dynamics and structure networks
-
Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S (2009) Allostery and conformational free energy changes in human tryptophanyl-TRNA synthetase from essential dynamics and structure networks. Proteins 78:506-517.
-
(2009)
Proteins
, vol.78
, pp. 506-517
-
-
Bhattacharyya, M.1
Ghosh, A.2
Hansia, P.3
Vishveshwara, S.4
-
9
-
-
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 USA 104:15711-15716.
-
(2007)
Proc Natl Acad Sci U.S.A.
, vol.104
, pp. 15711-15716
-
-
Ghosh, A.1
Vishveshwara, S.2
-
10
-
-
79960284776
-
Probing the allosteric mechanism in pyrrolysyl-TRNA synthetase using energy-Weighted network formalism
-
Bhattacharyya M, Vishveshwara S (2011) Probing the allosteric mechanism in pyrrolysyl-TRNA synthetase using energy-Weighted network formalism. Biochemistry 50:6225-6236.
-
(2011)
Biochemistry
, vol.50
, pp. 6225-6236
-
-
Bhattacharyya, M.1
Vishveshwara, S.2
-
11
-
-
84871305258
-
Interaction signatures stabilizing the NAD(P)-Binding Rossmann fold: A structure network approach
-
Bhattacharyya M, Upadhyay R, Vishveshwara S (2012) Interaction signatures stabilizing the NAD(P)-Binding Rossmann fold: A structure network approach. PLoS One 7:e51676.
-
(2012)
PLoS One
, vol.7
-
-
Bhattacharyya, M.1
Upadhyay, R.2
Vishveshwara, S.3
-
12
-
-
55249123363
-
Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes
-
Ghosh A, Vishveshwara S (2008) Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry 47:11398-11407.
-
(2008)
Biochemistry
, vol.47
, pp. 11398-11407
-
-
Ghosh, A.1
Vishveshwara, S.2
-
14
-
-
79959260870
-
Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-Ligand interactions
-
Bhattacharyya M, Vishveshwara S (2011) Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-Ligand interactions. Mol BioSyst 7:2320-2330.
-
(2011)
Mol BioSyst
, vol.7
, pp. 2320-2330
-
-
Bhattacharyya, M.1
Vishveshwara, S.2
-
16
-
-
77949609215
-
Atomic interaction networks in the core of protein domains and their native folds
-
Soundararajan V, Raman R, Raguram S, Sasisekharan V, Sasisekharan R (2010) Atomic interaction networks in the core of protein domains and their native folds. PLoS One 5:e9391.
-
(2010)
PLoS One
, vol.5
-
-
Soundararajan, V.1
Raman, R.2
Raguram, S.3
Sasisekharan, V.4
Sasisekharan, R.5
-
17
-
-
0036545421
-
Protein structure comparison using bipartite graph matching and its application to protein structure classification
-
Taylor WR (2002) Protein structure comparison using bipartite graph matching and its application to protein structure classification. Mol Cell Proteomics 1:334-339.
-
(2002)
Mol Cell Proteomics
, vol.1
, pp. 334-339
-
-
Taylor, W.R.1
-
18
-
-
84863714853
-
Insights into the fold organization of TIM barrel from interaction energy based structure networks
-
Vijayabaskar MS, Vishveshwara S (2012) Insights into the fold organization of TIM barrel from interaction energy based structure networks. PLoS Comput Biol 8:e1002505.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Vijayabaskar, M.S.1
Vishveshwara, S.2
-
19
-
-
38949190032
-
Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-Based rescue mutant design
-
Liu J, Nussinov R (2008) Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-Based rescue mutant design. Proc Natl Acad Sci USA 105:901-906.
-
(2008)
Proc Natl Acad Sci U.S.A.
, vol.105
, pp. 901-906
-
-
Liu, J.1
Nussinov, R.2
-
20
-
-
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
-
21
-
-
70350464948
-
Allosteric modulators of G proteincoupled receptors: Future therapeutics for complex physiological disorders
-
Wang L, Martin B, Brenneman R, Luttrell LM, Maudsley S (2009) Allosteric modulators of G proteincoupled receptors: Future therapeutics for complex physiological disorders. J Pharmacol Exp Ther 331:340-348.
-
(2009)
J Pharmacol Exp Ther
, vol.331
, pp. 340-348
-
-
Wang, L.1
Martin, B.2
Brenneman, R.3
Luttrell, L.M.4
Maudsley, S.5
-
22
-
-
38349164409
-
Computing topological parameters of biological networks
-
Assenov Y, Ram-rez F, Schelhorn S-E, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24:282-284.
-
(2008)
Bioinformatics
, vol.24
, pp. 282-284
-
-
Assenov, Y.1
Ram-Rez, F.2
Schelhorn, S.-E.3
Lengauer, T.4
Albrecht, M.5
-
24
-
-
84869418186
-
NetworkView: 3D display and analysis of protein-RNA interaction networks
-
Eargle J, Luthey-Schulten Z (2012) NetworkView: 3D display and analysis of protein-RNA interaction networks. Bioinformatics 28:3000-3001.
-
(2012)
Bioinformatics
, vol.28
, pp. 3000-3001
-
-
Eargle, J.1
Luthey-Schulten, Z.2
-
25
-
-
84864205788
-
Pyder: A PyMOL plugin to analyze coupled residues and their networks in protein structures
-
Pasi M, Tiberti M, Arrigoni A, Papaleo E (2012) xPyder: A PyMOL plugin to analyze coupled residues and their networks in protein structures. J Chem Inf Model 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
-
26
-
-
79955059412
-
GraProStr-Graphs of protein structures: A tool for constructing the graphs and generating graph parameters for protein structures
-
Vijayabaskar MS, Niranjan V, Vishveshwara S (2011) GraProStr-Graphs of protein structures: A tool for constructing the graphs and generating graph parameters for protein structures. Open Bioinform J 5:53-58.
-
(2011)
Open Bioinform J
, vol.5
, pp. 53-58
-
-
Vijayabaskar, M.S.1
Niranjan, V.2
Vishveshwara, S.3
-
27
-
-
30044437590
-
Mechanistic insight into the allosteric activation of a ubiquitinconjugating enzyme by RING-Type ubiquitin ligases
-
Ozkan E, Yu H, Deisenhofer J (2005) Mechanistic insight into the allosteric activation of a ubiquitinconjugating enzyme by RING-Type ubiquitin ligases. Proc Natl Acad Sci USA 102:18890-18895.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 18890-18895
-
-
Ozkan, E.1
Yu, H.2
Deisenhofer, J.3
-
28
-
-
80051658642
-
Crystal structure of the [bgr]2 adrenergic receptor-Gs protein complex
-
Rasmussen SGF, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, et al. (2011) Crystal structure of the [bgr]2 adrenergic receptor-Gs protein complex. Nature 477:549-555.
-
(2011)
Nature
, vol.477
, pp. 549-555
-
-
Rasmussen, S.G.F.1
Devree, B.T.2
Zou, Y.3
Kruse, A.C.4
Chung, K.Y.5
Kobilka, T.S.6
Thian, F.S.7
Chae, P.S.8
Pardon, E.9
Calinski, D.10
-
29
-
-
36448995359
-
High-Resolution crystal structure of an engineered human b2-Adrenergic G protein-Coupled receptor
-
Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi H-J, Kuhn P, Weis WI, Kobilka BK, et al. (2007) High-Resolution crystal structure of an engineered human b2-Adrenergic G protein-Coupled receptor. Science 318:1258-1265.
-
(2007)
Science
, vol.318
, pp. 1258-1265
-
-
Cherezov, V.1
Rosenbaum, D.M.2
Hanson, M.A.3
Rasmussen, S.G.F.4
Thian, F.S.5
Kobilka, T.S.6
Choi, H.-J.7
Kuhn, P.8
Weis, W.I.9
Kobilka, B.K.10
-
30
-
-
0037512360
-
Structural basis for orthogonal tRNA specificities of tyrosyl-TRNA synthetases for genetic code expansion
-
Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S (2003) Structural basis for orthogonal tRNA specificities of tyrosyl-TRNA synthetases for genetic code expansion. Nat Struct Mol Biol 10:425-432.
-
(2003)
Nat Struct Mol Biol
, vol.10
, pp. 425-432
-
-
Kobayashi, T.1
Nureki, O.2
Ishitani, R.3
Yaremchuk, A.4
Tukalo, M.5
Cusack, S.6
Sakamoto, K.7
Yokoyama, S.8
-
31
-
-
36049019300
-
Three-Dimensional structure of the ternary complex of yeast tyrosyl-TRNA synthetase
-
Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT (2004) Three-Dimensional structure of the ternary complex of yeast tyrosyl-TRNA synthetase. Nucleic Acids Symp Ser 48:155-156.
-
(2004)
Nucleic Acids Symp ser
, vol.48
, pp. 155-156
-
-
Tsunoda, M.1
Kusakabe, Y.2
Tanaka, N.3
Ohno, S.4
Nakamura, M.5
Senda, T.6
Sekine, M.7
Yokogawa, T.8
Nishikawa, K.9
Nakamura, K.T.10
-
32
-
-
0037099498
-
Class i tyrosyl-TRNA synthetase has a class II mode of cognate tRNA recognition
-
Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S (2002) Class I tyrosyl-TRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J 21:3829-3840.
-
(2002)
EMBO J
, vol.21
, pp. 3829-3840
-
-
Yaremchuk, A.1
Kriklivyi, I.2
Tukalo, M.3
Cusack, S.4
-
33
-
-
33645830948
-
CFinder: Locating cliques and overlapping modules in biological networks
-
Adamcsek B, Palla G, Farkas I, Der-Enyi I, Vicsek T (2006) CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics 22:1021-1023.
-
(2006)
Bioinformatics
, vol.22
, pp. 1021-1023
-
-
Adamcsek, B.1
Palla, G.2
Farkas, I.3
Der-Enyi, I.4
Vicsek, T.5
-
35
-
-
84873685831
-
Molecular signatures of G-Protein-Coupled receptors
-
Venkatakrishnan AJ, Deupi X, Lebon G, Tate CG, Schertler GF, Babu MM (2013) Molecular signatures of G-Protein-Coupled receptors. Nature 494:185-194.
-
(2013)
Nature
, vol.494
, pp. 185-194
-
-
Venkatakrishnan, A.J.1
Deupi, X.2
Lebon, G.3
Tate, C.G.4
Schertler, G.F.5
Babu, M.M.6
-
37
-
-
52949154680
-
Development of tRNA synthetases and connection to genetic code and disease
-
Schimmel P (2008) Development of tRNA synthetases and connection to genetic code and disease. Protein Sci 17:1643-1652.
-
(2008)
Protein Sci
, vol.17
, pp. 1643-1652
-
-
Schimmel, P.1
-
38
-
-
0024406896
-
Structure of tyrosyl-TRNA synthetase refined at 2.3 A ° resolution: Interaction of the enzyme with the tyrosyl adenylate intermediate
-
Brick P, Bhat TN, Blow DM (1989) Structure of tyrosyl-TRNA synthetase refined at 2.3 A ° resolution: Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol 208:83-98.
-
(1989)
J Mol Biol
, vol.208
, pp. 83-98
-
-
Brick, P.1
Bhat, T.N.2
Blow, D.M.3
-
39
-
-
0027968068
-
Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-Specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-Specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
40
-
-
17644392830
-
TM-Align: A protein structure alignment algorithm based on the TM-Score
-
Zhang Y, Skolnick J (2005) TM-Align: A protein structure alignment algorithm based on the TM-Score. Nucleic Acids Res 33:2302-2309.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
41
-
-
72949085966
-
Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks
-
Hansia P, Ghosh A, Vishveshwara S (2009) Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. Mol BioSyst 5:1860-1872.
-
(2009)
Mol BioSyst
, vol.5
, pp. 1860-1872
-
-
Hansia, P.1
Ghosh, A.2
Vishveshwara, S.3
-
42
-
-
34247580211
-
Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication
-
Atilgan AR, Turgut D, Atilgan C (2007) Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys J 92:3052-3062.
-
(2007)
Biophys J
, vol.92
, pp. 3052-3062
-
-
Atilgan, A.R.1
Turgut, D.2
Atilgan, C.3
-
43
-
-
80053590126
-
Computational modeling of allosteric communication reveals organizing principles of mutation-Induced signaling in ABL and EGFR kinases
-
Dixit A, Verkhivker GM (2011) Computational modeling of allosteric communication reveals organizing principles of mutation-Induced signaling in ABL and EGFR kinases. PLoS Comput Biol 7:e1002179.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Dixit, A.1
Verkhivker, G.M.2
-
44
-
-
61449101487
-
Allosteric communication occurs via networks of tertiary and quaternary motions in proteins
-
Daily MD, Gray JJ (2009) Allosteric communication occurs via networks of tertiary and quaternary motions in proteins. PLoS Comput Biol 5:e1000293.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Daily, M.D.1
Gray, J.J.2
-
45
-
-
34247186195
-
-
University of California San Francisco
-
Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke V, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WH, Kollman PA. AMBER 9 (2006) University of California, San Francisco.
-
(2006)
AMBER 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling III, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
Walker, R.C.11
Zhang, W.12
Wang, B.13
Hayik, S.14
Roitberg, A.15
Seabra, G.16
Wong, K.F.17
Paesani, F.18
Wu, X.19
Brozell, S.20
Tsui, V.21
Gohlke, V.22
Yang, L.23
Tan, C.24
Mongan, J.25
Hornak, V.26
Cui, G.27
Beroza, P.28
Mathews, D.H.29
Schafmeister, C.30
Ross, W.H.31
Kollman, P.A.32
more..
-
46
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case D, Cheatham T, Darden T, Gohlke H, Luo R, Merz K, Jr, Onufriev A, Simmerling C, Wang B, Woods R (2005) The Amber biomolecular simulation programs. J Comp Chem 26:1668-1688.
-
(2005)
J Comp Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.1
Cheatham, T.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.6
Onufriev Jr., A.7
Simmerling, C.8
Wang, B.9
Woods, R.10
-
47
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, loadbalanced, and scalable molecular simulation
-
Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, loadbalanced, and scalable molecular simulation. J Chem Theory Comput 4:435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
48
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
49
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
Bahar I, Lezon TR, Yang L-W, Eyal E (2010) Global dynamics of proteins: Bridging between structure and function. Annu Rev Biophys 39:23-42.
-
(2010)
Annu Rev Biophys
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.-W.3
Eyal, E.4
-
50
-
-
0029000696
-
Knowledge-Based potentials for proteins
-
Sippl MJ (1995) Knowledge-Based potentials for proteins. Curr Opin Struct Biol 5:229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
51
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814-818.
-
(2005)
Nature
, vol.435
, pp. 814-818
-
-
Palla, G.1
Derenyi, I.2
Farkas, I.3
Vicsek, T.4
-
52
-
-
70350031205
-
Understanding protein structure from a percolation perspective
-
Deb D, Vishveshwara S, Vishveshwara S (2009) Understanding protein structure from a percolation perspective. Biophys J 97:1787-1794.
-
(2009)
Biophys J
, vol.97
, pp. 1787-1794
-
-
Deb, D.1
Vishveshwara, S.2
Vishveshwara, S.3
-
53
-
-
0002687371
-
The small world problem
-
Milgram S (1967) The small world problem. Psychol Today 2:60-67.
-
(1967)
Psychol Today
, vol.2
, pp. 60-67
-
-
Milgram, S.1
-
54
-
-
7444234761
-
Solution structure of the ubiquitin-Conjugating enzyme UbcH5B
-
Houben K, Dominguez C, van Schaik FMA, Timmers HTM, Bonvin AMJJ, Boelens R (2004) Solution structure of the ubiquitin-Conjugating enzyme UbcH5B. J Mol Biol 344:513-526.
-
(2004)
J Mol Biol
, vol.344
, pp. 513-526
-
-
Houben, K.1
Dominguez, C.2
Van Schaik, F.M.A.3
Timmers, H.T.M.4
Bonvin, A.M.J.J.5
Boelens, R.6
|