-
1
-
-
82455175695
-
The golden age of GPCR structural biology: Any impact on drug design?
-
Kolb P, Klebe G (2011) The golden age of GPCR structural biology: Any impact on drug design? Angew Chem Int Edit 50:11573-11575.
-
(2011)
Angew Chem Int Edit
, vol.50
, pp. 11573-11575
-
-
Kolb, P.1
Klebe, G.2
-
2
-
-
79960176452
-
Progress in structure based drug design for G protein-coupled receptors
-
Congreve M, Langmead CJ, Mason JS, Marshall FH (2011) Progress in structure based drug design for G protein-coupled receptors. J Med Chem 54:4283-4311.
-
(2011)
J Med Chem
, vol.54
, pp. 4283-4311
-
-
Congreve, M.1
Langmead, C.J.2
Mason, J.S.3
Marshall, F.H.4
-
3
-
-
1242276192
-
Roles of G-proteincoupled receptor dimerization
-
Terrillon S, Bouvier M (2004) Roles of G-proteincoupled receptor dimerization. EMBO Rep 5:30-34.
-
(2004)
EMBO Rep
, vol.5
, pp. 30-34
-
-
Terrillon, S.1
Bouvier, M.2
-
4
-
-
80052027428
-
Asymmetry of GPCR oligomers supports their functional relevance
-
Maurice P, Kamal M, Jockers R (2011) Asymmetry of GPCR oligomers supports their functional relevance. Trends Pharmacol Sci 32:514-520.
-
(2011)
Trends Pharmacol Sci
, vol.32
, pp. 514-520
-
-
Maurice, P.1
Kamal, M.2
Jockers, R.3
-
6
-
-
72449147362
-
Dimerization in GPCR mobility and signaling
-
Lohse MJ (2010) Dimerization in GPCR mobility and signaling. Curr Opin Pharmacol 10:53-58.
-
(2010)
Curr Opin Pharmacol
, vol.10
, pp. 53-58
-
-
Lohse, M.J.1
-
7
-
-
84873155972
-
BRET and Time-resolved FRET strategy to study GPCR oligomerization: From cell lines toward native tissues
-
Cottet M, Faklaris O, Maurel D, Scholler P, Doumazane E, Trinquet, E, Pin, J, Durroux T (2012) BRET and Time-resolved FRET strategy to study GPCR oligomerization: From cell lines toward native tissues. Front Endocrinol (Lausanne) 3:92.
-
(2012)
Front Endocrinol (Lausanne)
, vol.3
, pp. 92
-
-
Cottet, M.1
Faklaris, O.2
Maurel, D.3
Scholler, P.4
Doumazane, E.5
Trinquet, E.6
Pin, J.7
Durroux, T.8
-
8
-
-
80053615320
-
The significance of G protein-coupled receptor crystallography for drug discovery
-
Salon JA, Lodowski DT, Palczewski K (2011) The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol Rev 63:901-937.
-
(2011)
Pharmacol Rev
, vol.63
, pp. 901-937
-
-
Salon, J.A.1
Lodowski, D.T.2
Palczewski, K.3
-
10
-
-
85027927015
-
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists
-
Wu B, Chien E, Mol C, Fenalti G, Liu W, Katritch, V, Abagyan, R, Brooun, A, Wells, P, Bi, CF, Hamel, DJ, Kuhn, P, Handel, TM, Cherezov, V, Stevens, RC (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330:1066-1071.
-
(2010)
Science
, vol.330
, pp. 1066-1071
-
-
Wu, B.1
Chien, E.2
Mol, C.3
Fenalti, G.4
Liu, W.5
Katritch, V.6
Abagyan, R.7
Brooun, A.8
Wells, P.9
Bi, C.F.10
Hamel, D.J.11
Kuhn, P.12
Handel, T.M.13
Cherezov, V.14
Stevens, R.C.15
-
11
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
Suel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10:59-69.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
12
-
-
1642304065
-
Structural determinants of allosteric ligand activation in RXR heterodimers
-
Shulman AI, Larson C, Mangelsdorf DJ, Ranganathan R (2004) Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116:417-429.
-
(2004)
Cell
, vol.116
, pp. 417-429
-
-
Shulman, A.I.1
Larson, C.2
Mangelsdorf, D.J.3
Ranganathan, R.4
-
13
-
-
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
-
14
-
-
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
-
15
-
-
84455167671
-
Hot spots for allosteric regulation on protein surfaces
-
Reynolds KA, McLaughlin RN, Ranganathan R (2011) Hot spots for allosteric regulation on protein surfaces. Cell 147:1564-1575.
-
(2011)
Cell
, vol.147
, pp. 1564-1575
-
-
Reynolds, K.A.1
McLaughlin, R.N.2
Ranganathan, R.3
-
16
-
-
44949105262
-
Exploring allosteric coupling in the alpha-subunit of Heterotrimeric G proteins using evolutionary and ensemble- based approaches
-
Sayar K, Ugur O, Liu T, Hilser VJ, Onaran O (2008) Exploring allosteric coupling in the alpha-subunit of Heterotrimeric G proteins using evolutionary and ensemble- based approaches. BMC Struct Biol 8:23.
-
(2008)
BMC Struct Biol
, vol.8
, pp. 23
-
-
Sayar, K.1
Ugur, O.2
Liu, T.3
Hilser, V.J.4
Onaran, O.5
-
17
-
-
31344432159
-
Determination of network of residues that regulate allostery in protein families using sequence analysis
-
Dima RI, Thirumalai D (2006) Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci 15:258-268.
-
(2006)
Protein Sci
, vol.15
, pp. 258-268
-
-
Dima, R.I.1
Thirumalai, D.2
-
18
-
-
84863780022
-
Characterization of the homodimerization interface and functional hotspots of the CXCR4 chemokine receptor
-
Rodriguez D, Gutierrez-de-Teran H (2012) Characterization of the homodimerization interface and functional hotspots of the CXCR4 chemokine receptor. Proteins 80:1919-1928.
-
(2012)
Proteins
, vol.80
, pp. 1919-1928
-
-
Rodriguez, D.1
Gutierrez-De-Teran, H.2
-
19
-
-
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
-
20
-
-
84861411420
-
Network-based models as tools hinting at nonevident protein functionality
-
Atilgan C, Okan OB, Atilgan AR (2012) Network-based models as tools hinting at nonevident protein functionality. Annu Rev Biophys 41:205-225.
-
(2012)
Annu Rev Biophys
, vol.41
, pp. 205-225
-
-
Atilgan, C.1
Okan, O.B.2
Atilgan, A.R.3
-
21
-
-
78651297517
-
GPCRDB: Information system for G proteincoupled receptors
-
Vroling B, Sanders M, Baakman C, Borrmann A, Verhoeven S, Klomp J, Oliveira L, de Vlieg J, Vriend G (2011) GPCRDB: information system for G proteincoupled receptors. Nucleic Acids Res 39:D309-D319.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Vroling, B.1
Sanders, M.2
Baakman, C.3
Borrmann, A.4
Verhoeven, S.5
Klomp, J.6
Oliveira, L.7
De Vlieg, J.8
Vriend, G.9
-
22
-
-
0037252680
-
GPCRDB information system for G protein-coupled receptors
-
Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003) GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res 31: 294-297.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 294-297
-
-
Horn, F.1
Bettler, E.2
Oliveira, L.3
Campagne, F.4
Cohen, F.E.5
Vriend, G.6
-
23
-
-
84860833500
-
Reorganizing the protein space at the universal protein resource (UniProt)
-
Consortium U (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40:D71-D75.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Consortium, U.1
-
24
-
-
39149100948
-
Stabilization of the human beta2-adrenergic receptor TM4-TM3- TM5 helix interface by mutagenesis of Glu122(3.41), a critical residue in GPCR structure
-
Roth CB, Hanson MA, Stevens RC (2008) Stabilization of the human beta2-adrenergic receptor TM4-TM3- TM5 helix interface by mutagenesis of Glu122(3.41), a critical residue in GPCR structure. J Mol Biol 376:1305-1319.
-
(2008)
J Mol Biol
, vol.376
, pp. 1305-1319
-
-
Roth, C.B.1
Hanson, M.A.2
Stevens, R.C.3
-
25
-
-
14244254079
-
Site-directed mutagenesis of CC chemokine receptor 1 reveals the mechanism of action of UCB 35625, a small molecule chemokine receptor antagonist
-
de Mendonca FL, da Fonseca PCA, Phillips RM, Saldanha JW, Williams TJ, Pease, JE (2005) Site-directed mutagenesis of CC chemokine receptor 1 reveals the mechanism of action of UCB 35625, a small molecule chemokine receptor antagonist. J Biol Chem 280: 4808-4816.
-
(2005)
J Biol Chem
, vol.280
, pp. 4808-4816
-
-
De Mendonca, F.L.1
Fonseca Pca, D.2
Phillips, R.M.3
Saldanha, J.W.4
Williams, T.J.5
Pease, J.E.6
-
26
-
-
0035876397
-
The Ile164 beta(2)-adrenoceptor polymorphism alters salmeterol exosite binding and conventional agonist coupling to G(s)
-
Green SA, Rathz DA, Schuster AJ, Liggett SB (2001) The Ile164 beta(2)-adrenoceptor polymorphism alters salmeterol exosite binding and conventional agonist coupling to G(s). Eur J Pharmacol 421:141-147.
-
(2001)
Eur J Pharmacol
, vol.421
, pp. 141-147
-
-
Green, S.A.1
Rathz, D.A.2
Schuster, A.J.3
Liggett, S.B.4
-
27
-
-
61449104961
-
Fragment-based identification of druggable 'hot spots' of proteins using fourier domain correlation techniques
-
Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S (2009) Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 25:621-627.
-
(2009)
Bioinformatics
, vol.25
, pp. 621-627
-
-
Brenke, R.1
Kozakov, D.2
Chuang, G.Y.3
Beglov, D.4
Hall, D.5
Landon, M.R.6
Mattos, C.7
Vajda, S.8
-
28
-
-
37249004920
-
Reaching for highhanging fruit in drug discovery at protein-protein interfaces
-
Wells JA, McClendon CL (2007) Reaching for highhanging fruit in drug discovery at protein-protein interfaces. Nature 450:1001-1009.
-
(2007)
Nature
, vol.450
, pp. 1001-1009
-
-
Wells, J.A.1
McClendon, C.L.2
-
29
-
-
81755184126
-
Allo-network drugs: Harnessing allostery in cellular networks
-
Nussinov R, Tsai CJ, 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
-
30
-
-
84877580262
-
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
-
PMID: 23384594
-
Csermely P, Korcsmaros T, Kiss HJ, London G, Nussinov R (2013) Structure and dynamics of molecular networks: A novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther PMID: 23384594.
-
(2013)
Pharmacol Ther
-
-
Csermely, P.1
Korcsmaros, T.2
Kiss, H.J.3
London, G.4
Nussinov, R.5
-
31
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
33
-
-
57349090665
-
Very fast prediction and rationalization of pK(a) values for proteinligand complexes
-
Bas DC, Rogers DM, Jensen JH (2008) Very fast prediction and rationalization of pK(a) values for proteinligand complexes. Proteins 73:765-783.
-
(2008)
Proteins
, vol.73
, pp. 765-783
-
-
Bas, D.C.1
Rogers, D.M.2
Jensen, J.H.3
-
34
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
35
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
Brooks BR, Brooks III CL, Mackerell AD, Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: The biomolecular simulation program. J Comput Chem 30:1545-1614.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
36
-
-
33846823909
-
Particle mesh ewald - An N.Log(N) method for ewald sums in large systems
-
Darden T, York D, Pedersen L (1993) Particle Mesh Ewald - an N.Log(N) Method for Ewald Sums in Large Systems. J Chem Phys 98:10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
37
-
-
45849143641
-
Dimerization of chemokine receptors in living cells: Key to receptor function and novel targets for therapy
-
Wang JH, Norcross M (2008) Dimerization of chemokine receptors in living cells: key to receptor function and novel targets for therapy. Drug Discov Today 13:625-632.
-
(2008)
Drug Discov Today
, vol.13
, pp. 625-632
-
-
Wang, J.H.1
Norcross, M.2
-
38
-
-
84859739224
-
Domain enhanced lookup time accelerated BLAST
-
Boratyn GM, Schaffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL (2012) Domain enhanced lookup time accelerated BLAST. Biol Direct 7:12.
-
(2012)
Biol Direct
, vol.7
, pp. 12
-
-
Boratyn, G.M.1
Schaffer, A.A.2
Agarwala, R.3
Altschul, S.F.4
Lipman, D.J.5
Madden, T.L.6
-
39
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
40
-
-
74549125386
-
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
-
Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221-224.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 221-224
-
-
Gouy, M.1
Guindon, S.2
Gascuel, O.3
-
41
-
-
0042826822
-
Independent component analysis: Algorithms and applications
-
Hyvarinen A, Oja E (2000) Independent component analysis: algorithms and applications. Neural Netw 13:411-430.
-
(2000)
Neural Netw
, vol.13
, pp. 411-430
-
-
Hyvarinen, A.1
Oja, E.2
-
42
-
-
78649334862
-
Independent component analysis: Mining microarray data for fundamental human gene expression modules
-
Engreitz JM, Daigle BJ Jr, Marshall JJ, Altman RB (2010) Independent component analysis: mining microarray data for fundamental human gene expression modules. J Biomed Inform 43:932-944.
-
(2010)
J Biomed Inform
, vol.43
, pp. 932-944
-
-
Engreitz, J.M.1
Daigle Jr., B.J.2
Marshall, J.J.3
Altman, R.B.4
-
43
-
-
80051785694
-
Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data
-
Yang L, Rau MH, Hoiby N, Molin S, Jelsbak L (2011) Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data. BMC Microbiol 11:184.
-
(2011)
BMC Microbiol
, vol.11
, pp. 184
-
-
Yang, L.1
Rau, M.H.2
Hoiby, N.3
Molin, S.4
Jelsbak, L.5
-
44
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
45
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, 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
|